diff --git a/automated_tool_installation_log.tsv b/automated_tool_installation_log.tsv index db75614ce..e5359c8a0 100644 --- a/automated_tool_installation_log.tsv +++ b/automated_tool_installation_log.tsv @@ -8148,3 +8148,8 @@ Update 221 27/11/24 02:31:03 krakentools_extract_kraken_reads False Installed iu Update 221 27/11/24 02:35:46 krakentools_kreport2krona False Installed iuc 02bbace216f2 02bbace216f2 2/2 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt Update 221 27/11/24 02:41:27 krakentools_kreport2mpa False Installed iuc d33cf727ed94 d33cf727ed94 3/3 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt Update 221 27/11/24 03:00:28 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_221/install_log.txt +Update 222 04/12/24 01:32:54 infernal False Tests failed bgruening 3711f654044e 3711f654044e Staging Testing 7/12 Annotation toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt +Update 222 04/12/24 01:38:59 krakentools_alpha_diversity False Tests failed iuc 78b69342c280 78b69342c280 Staging Testing 3/5 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt +Update 222 04/12/24 01:39:44 phyloseq_from_dada2 False Installed iuc 40ebae5bbe51 40ebae5bbe51 Metagenomic Analysis toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt +Update 222 04/12/24 01:53:31 quast False Tests failed iuc a3b35edea53a a3b35edea53a Staging Testing 11/13 Assembly toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt +Update 222 04/12/24 02:16:45 ucsc_fatovcf False Installed iuc a40dd4fd3096 a40dd4fd3096 2/2 Convert Formats toolshed.g2.bx.psu.edu /var/lib/jenkins/galaxy_tool_automation/update_build_222/install_log.txt diff --git a/staging.gvl.org.au/annotation.yml b/staging.gvl.org.au/annotation.yml index 1b577ead9..33386f610 100644 --- a/staging.gvl.org.au/annotation.yml +++ b/staging.gvl.org.au/annotation.yml @@ -2,11 +2,11 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - 6e9aea89e388 - 4efdca267d51 - - c2ef298da409 - 78c75f134c16 + - 3f3e247c053d + - c2ef298da409 + - 6e9aea89e388 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 @@ -19,8 +19,8 @@ tools: - name: aegean_gaeval owner: iuc revisions: - - 8dc7512c9dc9 - 1dd7adc21b6d + - 8dc7512c9dc9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_locuspocus @@ -33,23 +33,23 @@ tools: - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - a79ee60b6926 - - b5d8e5475247 - - fe3ca740a485 - - 4f2967b27e67 - - 1aae04680c4b - - 133f36c29579 - 3e1f6f6d557e - 44018dd6b447 + - 4f2967b27e67 - cd2480f35935 + - b5d8e5475247 + - 133f36c29579 + - fe3ca740a485 - f29602ae449e + - a79ee60b6926 + - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,36 +62,36 @@ tools: - name: augustus_training owner: bgruening revisions: - - f1e653756174 - 6519ebe25019 - - 7be22100e5e1 - dc027fa56d55 + - 7be22100e5e1 + - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus owner: bgruening revisions: - 28433faa6e42 - - ca6d970d931c - bd0e53f3a891 + - ca6d970d931c - 09855551d713 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - 92eee5f31117 - - 728dacaf08a9 - d77802fe76f7 + - 728dacaf08a9 - da5f1924bb2e + - 92eee5f31117 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap owner: iuc revisions: + - 7355bbf5e05f - fe48aa4ccd5e - 8fd427007e93 - - 7355bbf5e05f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: braker3 @@ -124,9 +124,9 @@ tools: - name: eggnog_mapper owner: galaxyp revisions: + - d9c3016f7283 - 9d1fbff733cf - 63662ae295d6 - - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -156,60 +156,60 @@ tools: - name: funannotate_annotate owner: iuc revisions: - - 3bbe70fef6df - b6b5cd37f2a2 - - 14f588312c56 - 756376aeb1ae - - 9f2455341fac + - 3bbe70fef6df - 9c15ca7e764e + - 9f2455341fac + - 14f588312c56 - 582fd74dc2a1 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - a230ea445788 - 8e1ace8f77c6 - - 989f7c061f35 - - 73428a792541 - - 1691af4a0d17 - 30fb23d4c31c + - 989f7c061f35 - 0ffe5be70caf + - a230ea445788 + - 1691af4a0d17 + - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - - 5a5ae61da69c - - e94187d661df - 494f0bb4a993 + - 5a5ae61da69c + - 30f08d74024f + - 563a19373357 - 0418d28136de + - e94187d661df - 57c6718cbfcc - - 563a19373357 - - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f77d7b685bb3 + - f31125bb85ea - 1bc5a03faf2e + - f77d7b685bb3 - d6c7106b7b2e - - f31125bb85ea - 2bba2ff070d9 - - 4b96ced19f75 - 7abc5f6dd595 + - 4b96ced19f75 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - b3cf4684e9c7 - 520e30695ec3 - - d3af38b9c7e1 + - fed64e676186 - 54961e026fe4 + - b3cf4684e9c7 + - d3af38b9c7e1 - d77fdcca400e - - fed64e676186 - 52af33194019 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -222,9 +222,9 @@ tools: - name: gff_to_prot owner: iuc revisions: - - 79261884facd - - 2aea122fbd25 - 07d7991bf205 + - 2aea122fbd25 + - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -237,9 +237,9 @@ tools: owner: iuc revisions: - ef2ad746b589 - - 602de62d995b - 8b3e3657034e - 43798b4caee0 + - 602de62d995b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -263,8 +263,8 @@ tools: - name: infernal owner: bgruening revisions: - - 477d829d3250 - c9e29ac5d099 + - 477d829d3250 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan @@ -297,19 +297,19 @@ tools: - name: maker owner: iuc revisions: - - d46d803ca6cc - - 3c1a01127868 - 370c210d9541 + - 3c1a01127868 + - d46d803ca6cc tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: - - b815ec682418 - - e95d52d295d7 + - 033755194fe9 - c8ac28e8ac44 + - e95d52d295d7 - 624606f7c996 - - 033755194fe9 + - b815ec682418 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mob_suite @@ -351,11 +351,11 @@ tools: - name: prokka owner: crs4 revisions: - - 8a22554cdde2 - a17498c603ec - - d643e3b03500 - - bf68eb663bc3 - eaee459f3d69 + - 8a22554cdde2 + - bf68eb663bc3 + - d643e3b03500 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: red @@ -367,15 +367,15 @@ tools: - name: repeat_masker owner: bgruening revisions: - - 3f987772e283 - ba6d2c32f797 + - 3f987772e283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: repeatmodeler owner: csbl revisions: - - 41bfbaf3c959 - 8661b2607b7e + - 41bfbaf3c959 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -400,14 +400,14 @@ tools: owner: iuc revisions: - cfcf33df7fc0 + - 68693743661e + - c7275bd8b4d6 + - 5c7b70713fb5 - 268d162b9c49 - 5b80f544c67f + - 5a29ab10dba6 - 6322be79bd8e - 8f92c2b26e6d - - 5a29ab10dba6 - - 68693743661e - - c7275bd8b4d6 - - 5c7b70713fb5 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift @@ -440,18 +440,18 @@ tools: - name: tbprofiler owner: iuc revisions: + - 809dfc93d593 - 45083d070fb8 - 8cb134b8c1a5 + - 37213cf56392 + - d03af1c7002c + - ba6f87115e13 + - 200c378d85f3 + - 037a11682176 - 4839e590cb26 - - ac8250086ac3 - - 809dfc93d593 - 51dd22484644 - - 037a11682176 - - 200c378d85f3 - - d03af1c7002c - e1a9d6fd258d - - ba6f87115e13 - - 37213cf56392 + - ac8250086ac3 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel diff --git a/staging.gvl.org.au/assembly.yml b/staging.gvl.org.au/assembly.yml index ae1b3ce05..9923dd013 100644 --- a/staging.gvl.org.au/assembly.yml +++ b/staging.gvl.org.au/assembly.yml @@ -2,45 +2,45 @@ tools: - name: abyss owner: iuc revisions: + - 7547fcab5d19 + - d6d5ccc2c581 + - db9b10824c61 - 0e93176640ac - - a929ce596a34 + - 841084c5fc46 - 8f1b150a2487 - - db9b10824c61 + - 0124fce4654a - 553bfe8bd0b5 - - fa5259cc561b - - d6d5ccc2c581 - - 841084c5fc46 - - 7547fcab5d19 - 890b794c997d - - 0124fce4654a + - a929ce596a34 + - fa5259cc561b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: + - b2860df42e16 - 94fe43e75ddc - b9e31c5c01c7 - - 21e491ad532a - - b2860df42e16 - ddddce450736 - 067592b6b312 + - 21e491ad532a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon owner: iuc revisions: - - 321347bd0494 - 25ca5d73aedf + - 321347bd0494 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bionano_scaffold owner: bgruening revisions: - - 3371c5bdc17a - 5258e18bbe23 - - a7f16f24e9a1 - - 22286dab5aa1 + - 3371c5bdc17a - faee8629b460 + - 22286dab5aa1 + - a7f16f24e9a1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit @@ -53,31 +53,31 @@ tools: - name: busco owner: iuc revisions: - - f18f0b887c31 - - 0d243f458b53 - - cf13a1e03e5b - - e5c372c91e46 - - e4bd1e99bacf + - e824f5d958d0 + - 1440ae06552f - 94170eee0ad8 - - 602fb8e63aa7 - 2dd755c1c6ff - - bb935709506a - 41030a6c03b7 - - 46ae58b1d792 + - cf13a1e03e5b + - 602fb8e63aa7 - 4048d82f0c88 - - 1440ae06552f - - 5ecdeca79a0d - - 1e62c28ba91d - - e824f5d958d0 + - f18f0b887c31 + - bb935709506a + - 46ae58b1d792 - ea8146ee148f + - e4bd1e99bacf + - 0d243f458b53 + - 5ecdeca79a0d - 2babe6d5c561 + - 1e62c28ba91d + - e5c372c91e46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - 86f150c8019d + - 5732f959936a - c5b7390290b1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -90,33 +90,33 @@ tools: - name: flye owner: bgruening revisions: - - cb8dfd28c16f + - 8d4f03b5fe9d + - e27815e82dd4 - 1ce9b1d72ec3 + - cb8dfd28c16f - 276f5d8712d5 - 3ee0ef312022 - - 1f0769f0b56b - - e27815e82dd4 - - 8d4f03b5fe9d - - 291923e6f276 - 3e4f8642c77e + - 291923e6f276 + - 1f0769f0b56b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - 01210c4e9144 - - 460fad600dce - b2f674562a18 - 3169a38c2656 + - 01210c4e9144 + - 460fad600dce tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: - - 06bcf65179fb - - 7348b69e5109 - 8b330a577046 + - 06bcf65179fb - ba88bc5a6446 + - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats @@ -124,10 +124,10 @@ tools: revisions: - 5127a713de83 - 6ec1b853c8fd + - 690c2caa367e - 3ef480892a9f - - 3fba9c77550a - f4a3eff8ab85 - - 690c2caa367e + - 3fba9c77550a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: hapcut2 @@ -139,24 +139,24 @@ tools: - name: hifiasm owner: bgruening revisions: + - da9d8bf98802 + - 71740308d412 + - f3c89da3af16 + - 284a1cb82b61 + - 5f625c63b8bc - 60024a528cbd - - 045c7c3d8e59 + - 41cea2aa2dce - 6505bd37670d - - 0ee0c3089254 - df25d4fb79b7 - - 71740308d412 - - 284a1cb82b61 - - 9ef6920c3089 - - f3c89da3af16 - ec9e21e9c71b - - 3f7be05a1597 - - da9d8bf98802 - - 41cea2aa2dce - 2061fb3b81b4 + - 045c7c3d8e59 - 5bec28269d95 - - 5f625c63b8bc - - 366a11d316a7 + - 9ef6920c3089 - 5161f204ba63 + - 0ee0c3089254 + - 366a11d316a7 + - 3f7be05a1597 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -174,20 +174,20 @@ tools: - name: megahit owner: iuc revisions: - - a96f3ad4e0d8 - - de387b2b2803 - 14ddfc8ffb93 + - a96f3ad4e0d8 - 7518ee87b53d + - de387b2b2803 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: - - 39edec572bae - - 9d79beb19ac3 + - f8113c25bc6b - d7edbc9c3a07 + - 9d79beb19ac3 + - 39edec572bae - eb7b00ec347d - - f8113c25bc6b - 09c589057ee8 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -195,22 +195,22 @@ tools: owner: iuc revisions: - 29dabd8db6f2 - - eadfd71dde37 - 51c2360aa807 + - eadfd71dde37 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f369ef5f210b - fd128c111ab0 - - 99ecfdafc64f + - f369ef5f210b + - 606b09cc9860 - 3ca2d2a9068c - - eb7a370f6588 - 2ecf5a570907 - - e731ea24e48d - - 606b09cc9860 - f338e9942b27 + - e731ea24e48d + - 99ecfdafc64f + - eb7a370f6588 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -222,9 +222,9 @@ tools: - name: miniasm owner: iuc revisions: - - a7b889b90140 - 8dee0218ac7d - b799a615995d + - a7b889b90140 - 8b6d0d85252b - 73a3846701e1 tool_panel_section_label: Assembly @@ -244,8 +244,8 @@ tools: - name: novoplasty owner: iuc revisions: - - 7c2f5268d01c - 64a1c751d99b + - 7c2f5268d01c - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu @@ -258,48 +258,47 @@ tools: - name: pretext_map owner: iuc revisions: - - 02831bf9e95f - - c6cec5ab35c1 - 2b16ba799da9 - - 79b48f02db49 - - dfb8a4497339 + - c6cec5ab35c1 - bbe19ef04a74 - - d256a51a656b - 8fef980d48b5 + - dfb8a4497339 + - 02831bf9e95f + - 79b48f02db49 + - d256a51a656b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: - 76d4cbefff85 - - e9bd16ba5ebd - a315c25dc813 + - e9bd16ba5ebd tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - - 875d0f36d66f - - a3b35edea53a + - 675488238c96 - 72472698a2df - - 59db8ea8c845 + - ebb0dcdb621a - 3061c8b029e5 + - 875d0f36d66f + - 342a1d1fed7b + - 59db8ea8c845 - 7594365c546b - - ebb0dcdb621a - - 675488238c96 - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: + - 39bed8de8017 - aa39b19ca11e + - 78c533842eeb + - cd06929b224b - d865b62f501c - a199cd7ac344 - - cd06929b224b - - 39bed8de8017 - - 78c533842eeb tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragoo @@ -317,12 +316,12 @@ tools: - name: raven owner: iuc revisions: + - 2b2a352488fa - f8564b2d7f63 - - 33b7d8481a76 - 5c55448d0f33 - - f11b994b7eb2 + - 33b7d8481a76 - 3edba9afc9bc - - 2b2a352488fa + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast @@ -335,13 +334,13 @@ tools: - name: rnaspades owner: iuc revisions: - - e122f9101584 - - 28189050e437 + - 5fc94b3a4704 - ef69617ecb42 - - 1d06c8b38e77 - 53c2bc8c2ae3 + - 1d06c8b38e77 + - 28189050e437 - 378e55aeeb25 - - 5fc94b3a4704 + - e122f9101584 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -353,191 +352,191 @@ tools: - name: shovill owner: iuc revisions: - - d9f6a00b6db7 - ad80238462c1 - - 83ead2be47b2 - - ee17a294d3a3 + - d9f6a00b6db7 + - f698c7604b3b - 865119fcb694 + - ee17a294d3a3 + - 83ead2be47b2 - 196a599ec43d - - f698c7604b3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: - - 24e471d13fe9 - 015283de3004 - 5e0825476fb7 + - 24e471d13fe9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - - 1bb12736175c - - 904bf932cf78 - 604782a8a53a - - 7490b213baa9 - 1fc82fe7ebef - - 051fd2db8a27 + - 1bb12736175c - c33a476f4001 + - 7490b213baa9 + - 904bf932cf78 + - 051fd2db8a27 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: - - fee85957cebe + - 9678993ca5bd - ad8b536d1caa - 655fa188c3cc - 808b3a0a6716 - - d6e617c4e338 - - 9678993ca5bd + - fee85957cebe - 34305b013402 + - d6e617c4e338 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - 7e27faaad80e - 037f9927c4ff - - b8002c3f7141 - 21da31ed41a1 - - 8d4b90bf9caf - - 7e27faaad80e - - e5a3b75a271f - 6b5a5842531e + - e5a3b75a271f + - 8d4b90bf9caf + - b8002c3f7141 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: - - f1532cb33c75 - - 2a10645aeadd - - 7922870efcca - 9de69775f512 - - 328aa71f0f3c - 5b26685e5d3b - 86f66ab58e14 + - f1532cb33c75 + - 2a10645aeadd + - 328aa71f0f3c + - 7922870efcca tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 1708851f8804 - e41dcb0e913b - - 8cc856b935ee + - 85fb02c43042 - 6aad515a5270 - 340bc17f49cf - - 85fb02c43042 + - 8cc856b935ee + - 1708851f8804 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_rnaviralspades owner: iuc revisions: - - de1260f8a300 - - d5fb354f745d - d159735a6a9f + - 6357b127161e - 249f6a28c751 - - b65a43f70b99 - b3490b036c5a - - 6357b127161e + - d5fb354f745d + - b65a43f70b99 + - de1260f8a300 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - d5887ace0dd4 - - 9006e5836729 - - b7829778729f - 33368fec3b70 + - 9006e5836729 + - d2d1df21dfb9 + - d5887ace0dd4 + - dd7ad84f3943 - 7897763d14ec - a90db5dbaaf3 - - dd7ad84f3943 - - d2d1df21dfb9 + - b7829778729f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 0368ac680e70 - 189e837009c9 - - 6f4c8ad6ea01 - - 8f631679571f - 505a9833ab5d + - 8f631679571f + - 0368ac680e70 - ced385aa976d + - 6f4c8ad6ea01 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - a7ed21de23fe - - 19bdfd1e6fe3 - - 9ded6109434a - d40ed4eb0c0e - - e59bee4565b3 + - 19bdfd1e6fe3 - 356afed970b4 + - a7ed21de23fe + - e59bee4565b3 + - 9ded6109434a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - - 80a17897564d - - ebd801e712bc + - 6dd935e4984b - b23249f81bc4 + - ebd801e712bc - 7673a6c920b2 - - 6dd935e4984b - 4688ae3b49b5 + - 80a17897564d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - ed312479d9eb + - b64696992ee9 - cb1e3db43020 - 59bd28f6265d - - 937ea677d437 - b5e35a2ca4f3 - - b64696992ee9 + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - 6015aa0303f2 - - 383bb5ad32e2 - 05bd7504fdb2 + - cb4768eeca3b - 2628f6790eda + - 383bb5ad32e2 - b9b0246a2be3 - - cb4768eeca3b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: - - 0a3a602cd1e3 - - 6e26c9afd301 - - 9e3e80cc4ad4 - 8f9f06995f98 - - 3e44ef016b45 - - e022dff952df - e92675014ac9 + - e022dff952df + - 9e3e80cc4ad4 + - 6e26c9afd301 + - 0a3a602cd1e3 + - 3e44ef016b45 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - 08256557922f - - 920677cd220f - 5da9a0e2fb2d + - 920677cd220f - 8d09f8be269e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: - - 4a53b89fa703 - 0e2b4e3f9ca1 + - 82398ba86ba7 - d81360ea69d8 + - 4a53b89fa703 - 37d88f41c810 - - 82398ba86ba7 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/staging.gvl.org.au/bacterial_typing.yml b/staging.gvl.org.au/bacterial_typing.yml index fa5523c0e..6d738cfa3 100644 --- a/staging.gvl.org.au/bacterial_typing.yml +++ b/staging.gvl.org.au/bacterial_typing.yml @@ -2,10 +2,10 @@ tools: - name: integron_finder owner: iuc revisions: - - 4768f7f8e93f - - 392f100eebcd - 1ae00120dd24 + - 4768f7f8e93f - bfd290fe1588 + - 392f100eebcd tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: islandpath @@ -17,17 +17,17 @@ tools: - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - - 1f5641a52664 - 31812e7a1315 - ded48b36f3b7 + - 1f5641a52664 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd owner: nml revisions: - - 24a7a95867b0 - - 5c8ff92e38a9 - 17fcac7ddf54 + - 5c8ff92e38a9 + - 24a7a95867b0 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bb_tools.yml b/staging.gvl.org.au/bb_tools.yml index e064325a6..cd35eb24e 100644 --- a/staging.gvl.org.au/bb_tools.yml +++ b/staging.gvl.org.au/bb_tools.yml @@ -2,14 +2,14 @@ tools: - name: bbtools_bbduk owner: iuc revisions: - - a9c9d768b751 + - 159b04e36791 - 0840ba83860c - - 1c427e24fb79 - 204a131e47db - - d58c27d2c5a7 - 7beb76ffbc0f - - 159b04e36791 - d1f62024a08b + - d58c27d2c5a7 + - 1c427e24fb79 + - a9c9d768b751 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge @@ -22,7 +22,7 @@ tools: - name: bbtools_tadpole owner: iuc revisions: - - ce13b4678f18 - 0ddf147d1897 + - ce13b4678f18 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/bed.yml b/staging.gvl.org.au/bed.yml index 440c1e6ba..3c93a52cf 100644 --- a/staging.gvl.org.au/bed.yml +++ b/staging.gvl.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 64e2edfe7a2c + - e19bebe96cd2 + - dde39ba9c031 + - 589e7e57fd6d + - 87ee588b3d45 - ce3c7f062223 + - 64e2edfe7a2c + - 07e8b80f278c - a1a923cd89e8 - a8eabd2838f6 - - 07e8b80f278c - - 0a5c785ac6db - - e19bebe96cd2 - - b28e0cfa7ba1 - a68aa6c1204a - - 589e7e57fd6d - - 87ee588b3d45 - - dde39ba9c031 + - b28e0cfa7ba1 + - 0a5c785ac6db tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/blast.yml b/staging.gvl.org.au/blast.yml index cca989b34..f26788125 100644 --- a/staging.gvl.org.au/blast.yml +++ b/staging.gvl.org.au/blast.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - f921014aba5a - - 62c9df8382c2 - e8ac2b53f262 - 54f751e413f4 + - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: diamond @@ -23,15 +23,15 @@ tools: - name: ncbi_blast_plus owner: devteam revisions: - - 2889433c7ae1 - 6f386c5dc4fb - - e25d3acf6e68 - - acf4e47b734c - - 0e3cf9594bb7 + - d999e774072a - 5edc472ec434 - - a52d2d93e595 - cbf3f518b668 - - d999e774072a + - a52d2d93e595 + - acf4e47b734c + - 0e3cf9594bb7 + - 2889433c7ae1 + - e25d3acf6e68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus diff --git a/staging.gvl.org.au/chemicaltoolbox.yml b/staging.gvl.org.au/chemicaltoolbox.yml index dfcecb47a..ca2f972b7 100644 --- a/staging.gvl.org.au/chemicaltoolbox.yml +++ b/staging.gvl.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - 095ad4d096d1 + - f4230f116196 - da6bd1975a71 - - c8cdde00b105 - - 6ca543ec1bf8 - 27ee142314a9 - - f4230f116196 - 710301bc46fa + - 095ad4d096d1 + - c8cdde00b105 + - 6ca543ec1bf8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -130,74 +130,74 @@ tools: - name: gmx_editconf owner: chemteam revisions: - - bfb65cb551d8 - - 88076940fa94 - - 0fac8e2afc13 - 79cfd9ead848 - 3b8a9d5ced85 + - 0fac8e2afc13 + - 88076940fa94 + - bfb65cb551d8 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - 55918daa5651 - eb6564a60136 - - 715cd0e87781 - f5d979cb4b54 - - d532b7e5f64b + - 55918daa5651 - b46d4b4d995c + - 715cd0e87781 + - d532b7e5f64b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: + - f26afd1b7104 - 5579659312e6 - - d2f955aea23a - fdf2cc80adb5 - - f26afd1b7104 - 97872d87ba80 + - d2f955aea23a tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - - d1d0efda35c0 - 319a28774da9 + - d1d0efda35c0 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - - ed736e6eee39 - 070e3ecc3fda - - 2c349b027a01 - - cac1886249a2 + - ed736e6eee39 - 4da9ee404eab + - cac1886249a2 + - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - 73008ef1f487 - - 2e219a2d9327 - - 807aa4c9293d - - d1f803b5943c - f197e34c33a9 - - 525ca7c8065f + - d1f803b5943c - c0c9a5024177 + - 525ca7c8065f - da8753545526 + - 73008ef1f487 + - 2e219a2d9327 + - 807aa4c9293d tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - c4fbab8e03c5 - - 61094e01eff9 + - 27ea4e1a3f95 + - 7568ae18908a - 1809414a9454 + - 61094e01eff9 - 2c8ed1b52bf7 - - 7568ae18908a - - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: - - ccfbd956a2d3 - d7ec25187599 - - ba83f0923369 - 730ef07b90ae - 79e8ab8f1e81 + - ccfbd956a2d3 + - ba83f0923369 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -268,10 +268,10 @@ tools: - name: openbabel_compound_convert owner: bgruening revisions: + - e6011617c748 + - 1400d1977e7b - 4242b4d68e9c - b59c91adeac1 - - 1400d1977e7b - - e6011617c748 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 75ee9c410951 - 7672039a0bb0 + - 75ee9c410951 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -297,15 +297,15 @@ tools: - name: qcxms_neutral_run owner: recetox revisions: - - 8f465c0c3b6c - 33b7a99b6de3 + - 8f465c0c3b6c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_production_run owner: recetox revisions: - - 356f7916ac07 - e97bfe7ac906 + - 356f7916ac07 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: rem_complex @@ -341,9 +341,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - d4c67ced6abc - bf99565cec1f - 9b48456a96fe + - d4c67ced6abc - 85fad59f8168 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/chip_seq.yml b/staging.gvl.org.au/chip_seq.yml index cea520d21..6308eadd7 100644 --- a/staging.gvl.org.au/chip_seq.yml +++ b/staging.gvl.org.au/chip_seq.yml @@ -4,8 +4,8 @@ tools: revisions: - 163688bb8f73 - f907216064f6 - - c97a786e8fb5 - fa56d93f7980 + - c97a786e8fb5 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: diffbind @@ -30,11 +30,11 @@ tools: - name: macs2 owner: iuc revisions: - - f5d67c722d67 + - 424aefbd7777 + - 86e2413cf3f8 - 640d3af5d833 - 495a4173006f - - 86e2413cf3f8 - - 424aefbd7777 + - f5d67c722d67 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: macs2 @@ -46,16 +46,16 @@ tools: - name: rnachipintegrator owner: pjbriggs revisions: - - 087d9872fb0d - b695071de766 + - 087d9872fb0d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer owner: devteam revisions: - - 5c2cc3b58c7d - - 4a14714649b4 - 74c9214cc8e6 + - 4a14714649b4 + - 5c2cc3b58c7d tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sicer diff --git a/staging.gvl.org.au/collection_operations.yml b/staging.gvl.org.au/collection_operations.yml index 27937c549..bc51fb7f2 100644 --- a/staging.gvl.org.au/collection_operations.yml +++ b/staging.gvl.org.au/collection_operations.yml @@ -2,17 +2,17 @@ tools: - name: bundle_collections owner: nml revisions: - - 705ebd286b57 - cd6da887a5f4 + - 705ebd286b57 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collapse_collections owner: nml revisions: + - 25136a2b0cfe + - 33151a38533a - 90981f86000f - 830961c48e42 - - 33151a38533a - - 25136a2b0cfe tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join @@ -31,16 +31,16 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 2dae863c8f42 - baabc30154cd - 6cbe2f30c2d7 - 0046692724f9 + - 2dae863c8f42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: unzip owner: imgteam revisions: - - 57f0914ddb7b - 38eec75fbe9b + - 57f0914ddb7b tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/convert_formats.yml b/staging.gvl.org.au/convert_formats.yml index c53d806d6..d42be1eca 100644 --- a/staging.gvl.org.au/convert_formats.yml +++ b/staging.gvl.org.au/convert_formats.yml @@ -2,9 +2,9 @@ tools: - name: agat owner: bgruening revisions: - - d6ede73082da - - abba05ead5d7 - e7449b2c14bf + - abba05ead5d7 + - d6ede73082da tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bed_to_protein_map @@ -17,38 +17,38 @@ tools: owner: iuc revisions: - 3b6f97e7094c - - e3cbd2287f63 - a3b86937ead6 + - e3cbd2287f63 + - 5e1240a87bcb - 4a6ee918c13a - - 6ef0b5664c69 + - 367b1ed91207 - ab9350a8ab4d - - 5e1240a87bcb - f3a19509108a - - 367b1ed91207 + - 6ef0b5664c69 - 0b3c3ad92827 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: + - 72ed72122deb - e525f9ffb9ac - - 091bb5922a82 - - 584008e574b2 - - d4d4e9febf5c + - e177a8ea0bf1 + - bd46669113b9 - 54ccb7e1f49a - - 501c21cce614 - 33c99804a32f + - 501c21cce614 + - 584008e574b2 - 1b5fc03380d4 - - 72ed72122deb - - bd46669113b9 - - e177a8ea0bf1 + - 091bb5922a82 + - d4d4e9febf5c tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 owner: iuc revisions: - - 11c3eb512633 - a0d092f27fdf + - 11c3eb512633 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: compress_file @@ -60,23 +60,23 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - e7ed3c310b74 - 7e801ab2b70e + - e7ed3c310b74 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: + - 77b41c89d856 - 186b8d913e6c - 8979c288aefb - - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 43807a65369f - 4b347702c4aa + - 43807a65369f - 614a63f14adf tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -89,8 +89,8 @@ tools: - name: gfa_to_fa owner: iuc revisions: - - e33c82b63727 - 8e9d604e92f4 + - e33c82b63727 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gffcompare_to_bed @@ -103,8 +103,8 @@ tools: owner: devteam revisions: - 154d00cbbf2d - - 4dea02886337 - 3e436657dcd0 + - 4dea02886337 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -122,8 +122,8 @@ tools: - name: mz_to_sqlite owner: galaxyp revisions: - - 705821bf30d2 - f5c632894818 + - 705821bf30d2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bam_to_cram @@ -136,39 +136,40 @@ tools: - name: tabular_to_fasta owner: devteam revisions: - - 0a7799698fe5 - 0b4e36026794 + - 0a7799698fe5 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - - 2dcfbbf9071a - 78fb18899c99 - 68f57cc8fad0 + - 2dcfbbf9071a tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 19e45916daf9 - b9b385097f13 + - 19e45916daf9 - 63769c4217a7 - - 92ac8e086317 - 26c6706bfb07 + - 92ac8e086317 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf owner: iuc revisions: + - a40dd4fd3096 - 3c19c84fbce2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_twobittofa owner: iuc revisions: - - 8067dfa00ed2 - e9bbe2f71784 + - 8067dfa00ed2 - 3c6f9e8a4c17 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -176,8 +177,8 @@ tools: owner: iuc revisions: - 98704d357ede - - a2f83a375bf2 - fa49730d1d4b + - a2f83a375bf2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: vcf2maf diff --git a/staging.gvl.org.au/deeptools.yml b/staging.gvl.org.au/deeptools.yml index b9e12cb66..3f811f3d6 100644 --- a/staging.gvl.org.au/deeptools.yml +++ b/staging.gvl.org.au/deeptools.yml @@ -3,33 +3,33 @@ tools: owner: bgruening revisions: - 268e91e540ee + - 5f6d123679f4 + - e821645ef8fc + - c929a006727f - de72ba3ed6f2 - a1ca9bccc7f2 - - e821645ef8fc - 29451af70c52 - - 5f6d123679f4 - - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 7a7fd0f5f15d + - bb1e4f63e0e6 - 0e143b4c3987 - 0e49b109abc2 - - 2d2cf5c1ea8a - - bb1e4f63e0e6 - 12af64f93288 + - 7a7fd0f5f15d + - 2d2cf5c1ea8a - 5d11599b8a7d tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - dc059492a995 - - 195e98217334 - 81b1e3e1fc6c + - 195e98217334 - c06951d10364 + - dc059492a995 - 1d848bc4585f - 7c1beb6d6eca tool_panel_section_label: DeepTools @@ -37,48 +37,48 @@ tools: - name: deeptools_bigwig_compare owner: bgruening revisions: - - 71aa86af6762 - - 3d211717a775 - - a67ac707496a + - 26e7304d6737 - 93eb012d9eed - - 07418a30ed01 - bfff7454b59a - - 26e7304d6737 + - 3d211717a775 + - 07418a30ed01 + - 71aa86af6762 + - a67ac707496a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 26983857c91a - 56d5b797ce84 - - 5be24eba848d - - 2bc10a9ca58b - dd0b7398bb96 + - 5be24eba848d - b8858746dc1f - - 26983857c91a - 29fcfd36e90a + - 2bc10a9ca58b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - c3e012dfe21f - - ee3a1b0f45f1 - - 72bfafe3330b - 9384cd033f30 - - e6d0bff01239 - 7ef978dc1b8a + - ee3a1b0f45f1 - 7e6bcd2e5128 + - c3e012dfe21f + - e6d0bff01239 + - 72bfafe3330b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - 514fa53b5efb - - fd1275e01605 - - 167788df3b46 - b73e213add0c - - 9470f29702f8 + - 167788df3b46 + - fd1275e01605 - d9a637e83828 + - 514fa53b5efb + - 9470f29702f8 - a60c359ec43c - fb9cf9c97ec4 tool_panel_section_label: DeepTools @@ -87,120 +87,120 @@ tools: owner: bgruening revisions: - ca0616bb2cdf - - 2c37ce318bc3 - - 5bffaa8354a1 - - 86febdcc4283 - - e479c7ca5570 - a02cfa31e9cb - c34d11ea4ba6 + - e479c7ca5570 + - 5bffaa8354a1 + - 2c37ce318bc3 + - 86febdcc4283 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 78f405266706 - - 2d466b530754 - 1fcb7adc39b8 - - 69a8621ca2f0 - - 192ef85c0b0b - 004aea905d4d + - 192ef85c0b0b - 01fb6a7654e6 + - 2d466b530754 + - 78f405266706 + - 69a8621ca2f0 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - d9ce4897dbb2 + - 2f9e4843f480 - d580d6acd1df - - 3c9f0c486cca - 9ecba5e225a6 - - db940c262830 - - 2f9e4843f480 - - 459cfa861f0b - 137c4beed34b + - 3c9f0c486cca + - 459cfa861f0b + - db940c262830 + - d9ce4897dbb2 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: + - f264afa9fa6f - fd408d755394 - - bad3ca889618 + - 2c66e43f1c86 - bd7db9e2f2cb - 32e451def88c - - 2c66e43f1c86 - - f264afa9fa6f + - bad3ca889618 - fbe773640707 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 4e12ea27f788 + - 231994413f89 - 56bce3c82278 + - 9368fbc49c8b + - 7fda5607e777 - 3b9d990a0a0e - 7e361d147872 - - 7fda5607e777 - - 9368fbc49c8b - - 231994413f89 + - 4e12ea27f788 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: - - 4431f39ede55 - - e65d16fb2724 + - ce4ce3316f74 - b1779366c8e9 + - 4431f39ede55 + - d9114ef1c8a5 - c03c3384cd81 - 94ca68515826 - - ce4ce3316f74 - - d9114ef1c8a5 + - e65d16fb2724 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - 2da482e408b8 - - b88ebb3672a1 - - 23f7c5f1fdaf - - f8fc4e5aff9d - 4ed32329e0ed + - f8fc4e5aff9d - d57251071381 + - b88ebb3672a1 + - 23f7c5f1fdaf - 793665fff0f8 + - 2da482e408b8 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - e4c7985d4585 - - ba6efa77fb79 + - 512155688d98 - 010e58e9d822 - - a4dfb122e52b + - a7849312d328 + - ba6efa77fb79 - 25d830337d31 - c60570fa602f - - 512155688d98 - - a7849312d328 + - e4c7985d4585 + - a4dfb122e52b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - c899e0ccff8c + - 38e3f226248b - 4d678170d29b + - aa200e4f3939 - 00d869ea03a1 - 69264da0ce77 - - 38e3f226248b - - aa200e4f3939 - 443d9a9d6d11 + - c899e0ccff8c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - - c361b12d207a - 6662b1a8d326 - a2d70c4fd406 + - c361b12d207a - 10301d137111 - d806504e96d9 + - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/dna_metabarcoding.yml b/staging.gvl.org.au/dna_metabarcoding.yml index f16285954..7148ee113 100644 --- a/staging.gvl.org.au/dna_metabarcoding.yml +++ b/staging.gvl.org.au/dna_metabarcoding.yml @@ -2,8 +2,8 @@ tools: - name: obi_annotate owner: iuc revisions: - - 3021b9f5809f - d50dc96e3ce9 + - 3021b9f5809f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean @@ -16,22 +16,22 @@ tools: - name: obi_convert owner: iuc revisions: - - 4d705e3443a7 - e328ced6cf0a + - 4d705e3443a7 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_grep owner: iuc revisions: - - e9e49cf06b42 - 02bab5ff7c37 + - e9e49cf06b42 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_illumina_pairend owner: iuc revisions: - - 8cb6bd511879 - 94f412098ac8 + - 8cb6bd511879 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_ngsfilter @@ -58,14 +58,14 @@ tools: - name: obi_tab owner: iuc revisions: - - 4cf47c504672 - 3299c7d5268f + - 4cf47c504672 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_uniq owner: iuc revisions: - - d4bea99366f9 - c0f7b58b4ce4 + - d4bea99366f9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/emboss.yml b/staging.gvl.org.au/emboss.yml index b265e8fe5..c87ebd957 100644 --- a/staging.gvl.org.au/emboss.yml +++ b/staging.gvl.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: + - 63dd26468588 - dba489bfcd62 - 832c20329690 - - 63dd26468588 - ce385837c160 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/epigenetics.yml b/staging.gvl.org.au/epigenetics.yml index 18d5fa26d..64123eae0 100644 --- a/staging.gvl.org.au/epigenetics.yml +++ b/staging.gvl.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - d82648ad25a3 - - cf1322aeb137 - 62f5fab76dfb - 6da3972210ee - 29bdbc353f20 + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene diff --git a/staging.gvl.org.au/fastafastq.yml b/staging.gvl.org.au/fastafastq.yml index 4156fe1b9..23693468f 100644 --- a/staging.gvl.org.au/fastafastq.yml +++ b/staging.gvl.org.au/fastafastq.yml @@ -8,26 +8,26 @@ tools: - name: cutadapt owner: lparsons revisions: - - c053d4cad713 - - 49370cb85f0f - - 4e5056fefd88 - - 5eb7e84243f2 - - b1c926deaa2d + - 64172f1c1202 - 8665bcc8b847 - 660cffd8d92a - - 44e2cc14f75b + - b1c926deaa2d - 8c0175e03cee - - c5e2e5902201 + - 44e2cc14f75b - 5915ea1ec9b1 - - de6cebe3c043 - - 64172f1c1202 - 093678460093 - - 135b80fb1ac2 - - fe74900d6dc7 + - 5eb7e84243f2 - c4b82dce8335 - - e4691e1589d3 + - 49370cb85f0f + - fe74900d6dc7 + - 135b80fb1ac2 - 48f587c13075 + - de6cebe3c043 + - e4691e1589d3 + - c053d4cad713 - 288f97432497 + - c5e2e5902201 + - 4e5056fefd88 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: cutadapt @@ -39,9 +39,9 @@ tools: - name: fasta_clipping_histogram owner: devteam revisions: + - 9db07fd39f85 - f666895cbebd - 8889eb864cef - - 9db07fd39f85 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram @@ -67,8 +67,8 @@ tools: - name: fasta_concatenate_by_species owner: devteam revisions: - - 717aee069681 - 25b8736c627a + - 717aee069681 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_extract @@ -80,16 +80,16 @@ tools: - name: fasta_filter_by_length owner: devteam revisions: - - e626b3ff9922 - 8cacfcf96a52 + - e626b3ff9922 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - - 516b97a23d7e - 859422bcb689 - 9457a20156db + - 516b97a23d7e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter @@ -101,16 +101,16 @@ tools: - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - 2904d46167da - f546e7278f04 + - 2904d46167da tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: + - f81d4362b6c1 - f773e98b26cf - ec0b5076173a - - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer @@ -122,10 +122,10 @@ tools: - name: fasta_stats owner: iuc revisions: - - 56022eb50bbd - - cd0874854f51 - - 0dbb995c7d35 - 9c620a950d3a + - 0dbb995c7d35 + - cd0874854f51 + - 56022eb50bbd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats @@ -137,14 +137,14 @@ tools: - name: fastp owner: iuc revisions: - - c59d48774d03 + - 1d8fe9bc4cb0 - dbfc505896e9 - - a626e8c0e1ba + - c59d48774d03 - d60c3f704da0 - - 1d8fe9bc4cb0 - dbf9c561ef29 - - ecb9f4854617 - 65b93b623c77 + - a626e8c0e1ba + - ecb9f4854617 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp @@ -156,9 +156,9 @@ tools: - name: fastq_combiner owner: devteam revisions: - - 9115b978ce10 - f1dc2a761c30 - b05e39b9c170 + - 9115b978ce10 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -170,9 +170,9 @@ tools: - name: fastq_filter owner: devteam revisions: + - 81a9090d6df3 - '144275714590' - 10b75444feae - - 81a9090d6df3 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_filter @@ -185,8 +185,8 @@ tools: owner: devteam revisions: - 8611b80a14d6 - - 47e5dbc3e790 - e9f8633db0a2 + - 47e5dbc3e790 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer @@ -198,8 +198,8 @@ tools: - name: fastq_manipulation owner: devteam revisions: - - 5b87038565bb - 7861f3b10c68 + - 5b87038565bb - e30352e889fe tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -213,8 +213,8 @@ tools: owner: devteam revisions: - 9dfda4e310ed - - 4e1d64e6385f - 9282652e7234 + - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality @@ -226,8 +226,8 @@ tools: - name: fastq_paired_end_deinterlacer owner: devteam revisions: - - 523c2aff0376 - 03d57fea6482 + - 523c2aff0376 - f3936d0632cb tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -240,9 +240,9 @@ tools: - name: fastq_paired_end_interlacer owner: devteam revisions: - - 3e396e702cea - - 2ccb8dcabddc - b41c2c1bcfbf + - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer @@ -268,10 +268,10 @@ tools: - name: fastq_paired_end_splitter owner: devteam revisions: - - 35e38452bb3f - e39cc71d3ed6 - - 249c8393f2d4 - 397dc333436b + - 35e38452bb3f + - 249c8393f2d4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter @@ -283,9 +283,9 @@ tools: - name: fastq_quality_converter owner: devteam revisions: + - 54053ea6c77e - 74db4cffab1f - 045f0e1043f7 - - 54053ea6c77e tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_quality_converter @@ -297,9 +297,9 @@ tools: - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - - f86c27295151 - f0e7deab6518 + - f86c27295151 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats @@ -311,9 +311,9 @@ tools: - name: fastq_trimmer owner: devteam revisions: - - f0b18efb97f1 - 33794bdb7fe0 - b63b2bfb3ea3 + - f0b18efb97f1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -332,10 +332,10 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - - 09070cacefd8 - 567d5b3c52b1 - d5e9e83cd3d8 + - 09070cacefd8 + - 529bccd5e4a1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_artifacts_filter @@ -347,8 +347,8 @@ tools: - name: fastx_barcode_splitter owner: devteam revisions: - - 8abdedf55101 - 4bedca26c133 + - 8abdedf55101 - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -361,8 +361,8 @@ tools: - name: fastx_clipper owner: devteam revisions: - - 736b8f6ee456 - 90858c306551 + - 736b8f6ee456 - bdf1ce174e39 - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ @@ -376,9 +376,9 @@ tools: - name: fastx_collapser owner: devteam revisions: + - 7ce1891db6f5 - 07497255281e - 421f0af4ee95 - - 7ce1891db6f5 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser @@ -390,10 +390,10 @@ tools: - name: fastx_renamer owner: devteam revisions: - - b29d37ca9e41 - 3599f5451ee2 - 02f8a17a4ebd - f984bb114520 + - b29d37ca9e41 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer @@ -406,8 +406,8 @@ tools: owner: devteam revisions: - 177f0621c266 - - 6027ef51ef91 - e246088b6e34 + - 6027ef51ef91 - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -420,10 +420,10 @@ tools: - name: fastx_trimmer owner: devteam revisions: - - 61b4cedc8934 - - 547e8d00f11c - 73194cdd4f57 + - 547e8d00f11c - 377ac2829eac + - 61b4cedc8934 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer @@ -447,9 +447,9 @@ tools: - name: pear owner: iuc revisions: - - f69501361cec - 037f0acc7830 - 2f804526f5fd + - f69501361cec - b4c6f054210a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -470,31 +470,31 @@ tools: owner: iuc revisions: - fdc21382376d - - 61eb4cfc7313 - 29ef2c5ec205 + - 61eb4cfc7313 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - fe1ae2ebf63d - - 795cd16de38f - 812705bcf39c + - 795cd16de38f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - 3da72230c066 - - 4b494533146a - a019807f4e67 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - - 4b494533146a - a019807f4e67 + - 4b494533146a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: split_paired_reads @@ -506,16 +506,16 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - dfa082f84068 - 51b771646466 + - dfa082f84068 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - 71f649c23021 - d3f58a0dc09d - bf04bd405d5b + - 71f649c23021 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit @@ -527,12 +527,12 @@ tools: - name: umi_tools_count owner: iuc revisions: + - 8250ea3a1501 - b557acca0b56 - - 71ad4a56c40c - - a535cf1e5da4 - e654095ab143 - 24013bf85a6f - - 8250ea3a1501 + - 71ad4a56c40c + - a535cf1e5da4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count @@ -551,14 +551,14 @@ tools: - name: umi_tools_extract owner: iuc revisions: - - 27ac32a22ad2 - - 7accf7407811 + - 7a7e33d28f62 - 9fa7803d1c51 - - f3759eec3018 + - 27ac32a22ad2 + - 828dba98cdb4 - 015cf18f4a15 - - 7a7e33d28f62 + - f3759eec3018 + - 7accf7407811 - 6a675c3aa610 - - 828dba98cdb4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract @@ -570,15 +570,15 @@ tools: - name: umi_tools_group owner: iuc revisions: - - 428735be9764 - d6255614afd7 + - 428735be9764 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_whitelist owner: iuc revisions: - - e4e12f0b3af1 - 4c8a1c7d3608 + - e4e12f0b3af1 - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fastq_quality_control.yml b/staging.gvl.org.au/fastq_quality_control.yml index 4460c17d5..83e8ce18c 100644 --- a/staging.gvl.org.au/fastq_quality_control.yml +++ b/staging.gvl.org.au/fastq_quality_control.yml @@ -4,8 +4,8 @@ tools: revisions: - e41385662e5e - 7b4468117008 - - ce9cd02d5b88 - 64e9a6afdd0c + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality @@ -18,14 +18,14 @@ tools: - name: fastqc owner: devteam revisions: - - e7b2202befea + - f2e8552cf1d0 + - 2c64fded1286 + - 5ec9f6bceaee - 3d0c7bdf12f5 - ff9530579d1f - - 5ec9f6bceaee - - 2c64fded1286 - - f2e8552cf1d0 - - 9da02be9c6cc - 2b0c9d9fc6ca + - e7b2202befea + - 9da02be9c6cc tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe @@ -47,38 +47,38 @@ tools: owner: devteam revisions: - 7306ec78632a - - 59003d0543cd - cc0fd298cc17 + - 59003d0543cd tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong owner: iuc revisions: - - a72af9de6bf5 - - 1f296803dfa3 - 8880fb74ef56 + - 1f296803dfa3 + - a72af9de6bf5 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: multiqc owner: iuc revisions: - - abfd8a6544d7 + - f7985e0479b9 - 75c93c70d094 - 5e33b465d8d5 + - 9a913cdee30e + - f7e2f1eb3a16 - 3d93dd18d9f8 - - f7985e0479b9 - - 1c2db0054039 - b2f1f75d49c4 + - 1c2db0054039 - bf675f34b056 - - f7e2f1eb3a16 - - 9a913cdee30e + - abfd8a6544d7 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: + - 084bbd8ba7b8 - cd7e644cae1d - 949f01671246 - - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/fetch_alignmentssequences.yml b/staging.gvl.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/staging.gvl.org.au/fetch_alignmentssequences.yml +++ b/staging.gvl.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/gemini_tools.yml b/staging.gvl.org.au/gemini_tools.yml index 95085422f..0439730c4 100644 --- a/staging.gvl.org.au/gemini_tools.yml +++ b/staging.gvl.org.au/gemini_tools.yml @@ -2,30 +2,30 @@ tools: - name: gemini_actionable_mutations owner: iuc revisions: - - 142d95ab942e - 3630a6e624d4 + - 142d95ab942e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_amend owner: iuc revisions: - - 4bd4870ecd33 - be828b79bd4d + - 4bd4870ecd33 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: - - 8f53b238a360 - f2f3bc622a16 + - 8f53b238a360 - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -45,8 +45,8 @@ tools: - name: gemini_de_novo owner: iuc revisions: - - 9db3e299b1c8 - d5b01cc263be + - 9db3e299b1c8 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_dump @@ -59,15 +59,15 @@ tools: - name: gemini_fusions owner: iuc revisions: - - 8151a5a0e4f6 - 91d53f89ca54 + - 8151a5a0e4f6 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_gene_wise owner: iuc revisions: - - 452104bdc655 - d46017ddbf94 + - 452104bdc655 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -79,8 +79,8 @@ tools: - name: gemini_interactions owner: iuc revisions: - - 184aa4e686e2 - 2550239feed5 + - 184aa4e686e2 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_load @@ -94,15 +94,15 @@ tools: - name: gemini_lof_sieve owner: iuc revisions: - - 90021fffff70 - 2969a1f43b7d + - 90021fffff70 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_mendel_errors owner: iuc revisions: - - 00c2734b3bea - 61343646155c + - 00c2734b3bea tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_pathways @@ -130,42 +130,42 @@ tools: - name: gemini_recessive_and_dominant owner: iuc revisions: - - 05124dc72dba - 86f3aac4418d + - 05124dc72dba tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_region owner: iuc revisions: - - 601b70d10d92 - 33efe43c1dbb + - 601b70d10d92 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_roh owner: iuc revisions: - - 93967598e18e - 345d41f3f574 + - 93967598e18e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_set_somatic owner: iuc revisions: - - ef9991a4a9a7 - e4e2128460e3 + - ef9991a4a9a7 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_stats owner: iuc revisions: - - 5c9efee9cb1e - ee894347fcd6 + - 5c9efee9cb1e tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/genome_editing.yml b/staging.gvl.org.au/genome_editing.yml index 2e186f768..2a6e45eeb 100644 --- a/staging.gvl.org.au/genome_editing.yml +++ b/staging.gvl.org.au/genome_editing.yml @@ -2,8 +2,8 @@ tools: - name: mageck_count owner: iuc revisions: - - e329d44424d7 - 3edbd1ff5602 + - e329d44424d7 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_gsea @@ -16,15 +16,15 @@ tools: - name: mageck_mle owner: iuc revisions: - - 26126538a86f - b36c85e37a48 + - 26126538a86f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test diff --git a/staging.gvl.org.au/get_data.yml b/staging.gvl.org.au/get_data.yml index dd2b28248..942851da2 100644 --- a/staging.gvl.org.au/get_data.yml +++ b/staging.gvl.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - e9df53a75f3c - b39347891609 - 983bf725dfc2 - c1b437242fee + - e9df53a75f3c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,53 +17,53 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - 28587613264f - - 1c58de56d587 - e063168e0a81 + - 1c58de56d587 + - 28587613264f tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 516a54ddf218 - - 7068f48d0ef9 - - e407b9da183a - - 653e89d73fc4 - - 9a776b080193 + - f5ea3ce9b9b0 - 69ebb7f46e45 + - e08a7ad4378b + - c441583adae5 + - 516a54ddf218 + - 734abc7ac21d - 83c7d564b128 - - 4317d3cb6cba - - 4df8de2d0e48 - aad3885b3216 - - 1ec814014652 - - e08a7ad4378b + - 9a776b080193 - 6ea73833cf67 - - 734abc7ac21d - - f5ea3ce9b9b0 - - f8054ea1c365 - - 8848455c0270 - - 1790dcf3c32d - - c441583adae5 + - 5e6237d58b0c + - 7068f48d0ef9 - ba931a59dd59 + - 653e89d73fc4 + - 1790dcf3c32d + - 8848455c0270 + - f8054ea1c365 + - 4df8de2d0e48 + - e407b9da183a + - 1ec814014652 + - 4317d3cb6cba - 6591f049cf7e - - 5e6237d58b0c tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 9aaa46d45472 - - 21a560af5913 - - 34758ab8aaa4 - 75b3b3d0adbf + - 34758ab8aaa4 + - 21a560af5913 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - - 468c71dac78a - - 054483e27a35 - bfdc6a7ffd3a + - 054483e27a35 + - 468c71dac78a - af5eccf83605 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/graphdisplay_data.yml b/staging.gvl.org.au/graphdisplay_data.yml index 81420649f..ebf64259a 100644 --- a/staging.gvl.org.au/graphdisplay_data.yml +++ b/staging.gvl.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - c4bde687c846 - - a64dc31ab7f2 - - 4b519282a05b - - ae9994cf526f - - 740057a5126d - df7356989ac1 - fd59d783248a + - 4b519282a05b - 7f13dc906cb9 - 290a11559985 + - 740057a5126d + - a64dc31ab7f2 + - ae9994cf526f + - c4bde687c846 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -34,9 +34,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 867ab348287d - - f95284aa2946 - 7cf5b1d072b5 + - f95284aa2946 + - 867ab348287d tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -48,24 +48,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: + - 51c6ccaace7e + - 53460afd5115 + - ca7cb0eaad62 - 374e9062d874 - - 48b42ee61bc5 - 3b37b1b1c3a7 + - 48b42ee61bc5 - '566197475670' - - 51c6ccaace7e - - ca7cb0eaad62 - - 53460afd5115 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - - d3a9e32672ec - - 391a4cc45fea - 10515715c940 - 1a72f938213e - - 3d059e9c2fba - da4c086cff5b + - d3a9e32672ec + - 3d059e9c2fba + - 391a4cc45fea tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -85,11 +85,11 @@ tools: - name: ggplot2_point owner: iuc revisions: - - 5fe1dc76176e - - 299307abd804 + - 1acf88921176 - d0fc8b746d57 - 5298e06f14f9 - - 1acf88921176 + - 299307abd804 + - 5fe1dc76176e - e3a675da7fd0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -136,17 +136,17 @@ tools: - name: jbrowse owner: iuc revisions: - - 6cd09d7b5f37 - - 17359b808b01 - - 4542035c1075 - - 2bb2e07a7a21 + - 1cfc579079a6 + - 836d1aa3e89a - 112eb40ba6cf - ca2def38369c - - 836d1aa3e89a + - 17359b808b01 - a6e57ff585c0 + - 2bb2e07a7a21 + - 6cd09d7b5f37 - 667e17248bfe - - 1cfc579079a6 - fd5dbf0f732e + - 4542035c1075 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -164,16 +164,16 @@ tools: - name: pathview owner: iuc revisions: + - 03c13085aecc - fe154a7af404 - f1691de443a7 - - 03c13085aecc tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - bd1416eea1f0 - 594b85e4237a + - bd1416eea1f0 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf @@ -187,10 +187,10 @@ tools: - name: plotly_ml_performance_plots owner: bgruening revisions: + - f234e2e59d76 + - 85da91bbdbfb - 1c5dcef5ce0f - 62e3a4e8c54c - - 85da91bbdbfb - - f234e2e59d76 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_parallel_coordinates_plot @@ -209,11 +209,11 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 7c9417381ad5 - 326098bc19cc - - 44c66e8d21e6 - 26f2fe7e53a1 + - 7c9417381ad5 - 6c571966cfb9 + - 44c66e8d21e6 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -225,23 +225,23 @@ tools: - name: pygenometracks owner: iuc revisions: - - 7dd841a32245 - 326a3db8d9d1 + - 360df4999907 + - 7dd841a32245 + - a1abfa420d9d - 4ac4e7083b7e - 2824d77cd8f8 - - a1abfa420d9d - 36b848d5f3ec - 14e7c35f3d00 - - 360df4999907 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot owner: iuc revisions: - - 83c573f2e73c + - 73b8cb5bddcd - 2f557f6abbfb - 44608d0193ed - - 73b8cb5bddcd + - 83c573f2e73c tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/staging.gvl.org.au/hca_single_cell.yml b/staging.gvl.org.au/hca_single_cell.yml index 795c95ffb..439f27bfb 100644 --- a/staging.gvl.org.au/hca_single_cell.yml +++ b/staging.gvl.org.au/hca_single_cell.yml @@ -8,8 +8,8 @@ tools: - name: gtf2gene_list owner: ebi-gxa revisions: - - 1a642de6db01 - 14b3f2a4523b + - 1a642de6db01 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: retrieve_scxa @@ -21,15 +21,15 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph owner: ebi-gxa revisions: - - 22bd5861706d - 7779b9dcf040 + - 22bd5861706d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter_cells @@ -49,22 +49,22 @@ tools: - name: scanpy_find_cluster owner: ebi-gxa revisions: - - fc4b3b46dc9d - 36735850e461 + - fc4b3b46dc9d tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 0a8e527d1517 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,30 +77,30 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 352cdf3b2f75 - 3c47bc560688 + - 352cdf3b2f75 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - 6903bc865d63 - c354af93f567 + - 6903bc865d63 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - - ff6decc0f432 - 9a2f72d7dbd2 + - ff6decc0f432 + - 94697510d55f tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 70cb0596ffef - 53ce0e336840 + - 70cb0596ffef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data @@ -113,29 +113,29 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - d4c9061c8fef - 73d43034c860 + - d4c9061c8fef tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 7d5c97823f8b - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet owner: ebi-gxa revisions: - - 4a74b45c1ce4 - 6f5509cf3176 + - 4a74b45c1ce4 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - cb1992d1804b - d3df472a21dc + - cb1992d1804b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x @@ -155,8 +155,8 @@ tools: - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -169,8 +169,8 @@ tools: - name: scanpy_run_fdg owner: ebi-gxa revisions: - - be019b069e31 - 65c3ec07502b + - be019b069e31 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_paga @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - 767a675b5254 + - 0f98603d0116 - ea91cfd0444e tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/hicexplorer.yml b/staging.gvl.org.au/hicexplorer.yml index 6d1f18499..73ec83f07 100644 --- a/staging.gvl.org.au/hicexplorer.yml +++ b/staging.gvl.org.au/hicexplorer.yml @@ -2,34 +2,34 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - - ed2cca6b5de4 - - 29f66c353bcb - - 0f611e7d7858 - a4c13ddcc8ee + - 29f66c353bcb - 921a2da49a0c + - ed2cca6b5de4 + - 9edf8894a22d + - 0f611e7d7858 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: + - d404277cc87a + - 755df866ad0c - ec4b948dc6f0 - 5746d61f0a91 - - d404277cc87a - - 11de0d28ab30 - 78fb5e286609 - - 755df866ad0c + - 11de0d28ab30 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 977dc15add20 - - f72063d9426b - 11fa44ee0603 - - 03dd3c16ae4e - - 4d511437b1e5 + - f72063d9426b + - 977dc15add20 - 9e357a8b2ec3 + - 4d511437b1e5 + - 03dd3c16ae4e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca @@ -37,21 +37,21 @@ tools: revisions: - 3b5b54ed6392 - 1da5f169b491 + - 77919cc3618e + - c3e5e2cf12b7 - 41dbf4d162a2 - 0ba4f56a3613 - - c3e5e2cf12b7 - - 77919cc3618e tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: + - f741330d4a71 + - 5308ca68ef3d - 9939786dd9c9 - b63363075c2e - 7babd8a46fe0 - 12d51d7be66f - - f741330d4a71 - - 5308ca68ef3d tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/staging.gvl.org.au/imaging.yml b/staging.gvl.org.au/imaging.yml index 92ac914a1..7849adca6 100644 --- a/staging.gvl.org.au/imaging.yml +++ b/staging.gvl.org.au/imaging.yml @@ -2,20 +2,20 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: - - 7db4fc31dbee - - 699a5e9146b3 - - 8bccb36e055a - - 81f0cbca04a7 - 0c777d708acc - 3df9f0a4bf34 + - 699a5e9146b3 + - 81f0cbca04a7 + - 8bccb36e055a + - 7db4fc31dbee tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - 2436a8807ad1 - - 5791a7f65275 - 0a53256b48c6 + - 5791a7f65275 - 5bc8cdc17fd0 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -30,27 +30,27 @@ tools: - name: 2d_histogram_equalization owner: imgteam revisions: - - 77f7159d775a - 70316d792fc9 - b1c2c210813c + - 77f7159d775a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - f70b215d155c - - d51310ab328a - dba87c4b32d3 + - d51310ab328a + - f70b215d155c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: bfconvert owner: imgteam revisions: - - 85edbb7a436b - - fcadded98e61 - f3360fbeda64 - - b07f4839ca77 - 10eed33aa9b2 + - 85edbb7a436b + - b07f4839ca77 + - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage @@ -72,23 +72,23 @@ tools: owner: bgruening revisions: - e917a2424690 - - 0e4dccaafef5 - eb6c08714244 + - 0e4dccaafef5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray owner: bgruening revisions: - - e8f822eeb9fd - bad171ed1e96 + - e8f822eeb9fd tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_common owner: bgruening revisions: - 670975e92458 - - 6070780813d9 - e7273daa5ae2 + - 6070780813d9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_convert_objects_to_image @@ -102,113 +102,113 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 6a7da2e5f696 + - 5d28ac336861 - 2484086dee41 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: + - bace5a93a97c - f2ed92b011a9 - 11f177b1a59e - - bace5a93a97c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: + - d0178bdcd00e - f8fa0f6718a3 - f24c370e5ea4 - - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: + - 3245681b2f6d - 31d195bedf6d - ad271f78a87a - - 3245681b2f6d tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_identify_primary_objects owner: bgruening revisions: - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - ff1a86a87364 - 6100a22bf4f2 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - b178453ea8d1 - - 3a05117669cf - 667a513e67e4 + - 3a05117669cf tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - ac5bea85a391 - 2564f461de62 - a1a961c46d4b + - ac5bea85a391 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_area_occupied owner: bgruening revisions: - - 20dbb1f7ec7b - 91e03287f285 + - 20dbb1f7ec7b - a32c3f810ade tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - - b64af54c5c09 - - 8536b1ae0254 - 5499dc6f8ac1 + - 8536b1ae0254 + - b64af54c5c09 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - 6f4715b8540a - - e972e07c7845 - d3890df07463 + - e972e07c7845 + - 6f4715b8540a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - e52c75a28c4b - 407925835dd9 - 980aed9e8fd5 - - e52c75a28c4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - 79e10d12d90a - acf3aa487283 - d85f11570109 + - 79e10d12d90a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: + - 80b200ae516b - b76841ee5560 - 035a58c7f54a - - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_overlay_outlines @@ -229,8 +229,8 @@ tools: owner: bgruening revisions: - 33f4fa1413fb - - 27edbb90ab2b - 4ecf93628f97 + - 27edbb90ab2b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile diff --git a/staging.gvl.org.au/ivar.yml b/staging.gvl.org.au/ivar.yml index 2dc31a415..c07f7df97 100644 --- a/staging.gvl.org.au/ivar.yml +++ b/staging.gvl.org.au/ivar.yml @@ -2,14 +2,14 @@ tools: - name: ivar_consensus owner: iuc revisions: - - e4ee04da1c19 - - 40737febe339 + - f362150bef41 - 78bbd17d0703 + - d6e72da3ec35 - 3e4f434a69c6 - - f362150bef41 - - a38934e303b9 + - 40737febe339 - 1069f6db0a0e - - d6e72da3ec35 + - e4ee04da1c19 + - a38934e303b9 - e319b5b65879 - 3a72fede57ce tool_panel_section_label: iVar @@ -17,78 +17,78 @@ tools: - name: ivar_filtervariants owner: iuc revisions: + - 7fe36019c073 - f91cfb73d369 - - c88553ec696e + - fcbeda41d0ac + - 2b95d5c04908 - 0135f1d487a0 + - 618297d23022 + - c88553ec696e - 8f8df367470d - - 72ddd32392cd - - 7fe36019c073 - - fcbeda41d0ac - 9537184d421f - - 618297d23022 - - 2b95d5c04908 + - 72ddd32392cd tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - 2cf4a1cafc16 + - ad0dc9f4c9e2 - fafb3d685fa9 + - 2cf4a1cafc16 - d7e79eb3bcb3 - - ad0dc9f4c9e2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 28a6f1908fcc - - 9eaadf03e0df - - 8d36959b000d - - 43aac8d29685 - - bd2a7d1316b9 - - 6a1515bb0687 + - 8c05afb547fa + - ee2beb764a7b + - ee29337f905c - 7f1cfa4c0e32 + - bd2a7d1316b9 - 94df24c6bc00 - 3d18f8c3c0f6 - - ee29337f905c - - 5dc33613c288 - - ee2beb764a7b - - 8c05afb547fa - a1c2aecd7a0d + - 8d36959b000d + - 5dc33613c288 + - 9eaadf03e0df + - 28a6f1908fcc + - 6a1515bb0687 + - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: - - 5d6ed46cc101 - - 5671e1d3d5ee - - 364f4ffec275 - - db536ad45f28 - - c092052ed673 - - 8858fa037a15 - - 9f978da6528a - - d37ede8589b2 - cb903c9dc33d + - db536ad45f28 - e3bb03cf207a + - d37ede8589b2 - 86a20ae274fc - bcaa0d571ce2 + - c092052ed673 + - 5d6ed46cc101 + - 364f4ffec275 + - 8858fa037a15 - a250929be21b + - 9f978da6528a + - 5671e1d3d5ee tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - 584beffa972b - - c5c9f02b6167 - 194e3ceee923 - 230b05597996 - - 38b91a3190cd - - ed28dd32141c + - f95f403841ad - e1a015876aa9 + - 3b6a16d82c1b + - 38b91a3190cd + - c5c9f02b6167 + - 12d66d0d05ac - abbc8041e8ec + - ed28dd32141c - 49236b03e4fd - - f95f403841ad - - 12d66d0d05ac - - 3b6a16d82c1b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/join_subtract_and_group.yml b/staging.gvl.org.au/join_subtract_and_group.yml index 84763b815..c5e46d293 100644 --- a/staging.gvl.org.au/join_subtract_and_group.yml +++ b/staging.gvl.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: + - f198773344e4 - b8a457820315 - 17e3b698dd52 - - f198773344e4 - 0f1724dd59d2 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - - a513e3fbb4c5 - ac092723240d - - 374cb875d38a - ba0c40780ecf + - 374cb875d38a + - a513e3fbb4c5 - 22c2a1ac7ae3 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/machine_learning.yml b/staging.gvl.org.au/machine_learning.yml index af82722ed..ca8b7279f 100644 --- a/staging.gvl.org.au/machine_learning.yml +++ b/staging.gvl.org.au/machine_learning.yml @@ -10,28 +10,28 @@ tools: - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - - 4d81e3e2fb63 - 8a794e6d3388 + - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - b6ef6d0cb6b7 - 2af1346e68c9 + - b6ef6d0cb6b7 - e1317b5502fa - - f1b9a42d6809 - 818f9b69d8a0 + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c + - 1588f9076e32 - 05143043ca13 - 947c2eacccb8 - - 1588f9076e32 + - c80db5d6fd8c - 8334dc98c48e tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu @@ -39,62 +39,62 @@ tools: owner: bgruening revisions: - 9991c4ddde14 - - 25b46af53232 - - 83228baae3c5 - - 1552b8cb4a94 - 29e4122c90de + - 1552b8cb4a94 + - 83228baae3c5 + - 25b46af53232 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: + - 841a6cc5fc58 - f3dfa4bdf87e - 060ca94ac049 - - a07ab242b0b5 - - 841a6cc5fc58 - 1a53edc4b438 + - a07ab242b0b5 - 53616c8b0865 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: + - dc4b5fd604a6 + - d4808d5b83da - 40f4447733b2 + - 2fc89dcd41c8 - 927586a18553 - 91c4e3331208 - - d4808d5b83da - - 2fc89dcd41c8 - - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 36e8d6d5d01b - - 301e07345c93 - 7626ea9c2e1b - - c6ae57f774c6 - 25ab6b4e376e + - 36e8d6d5d01b - e5a5ad882f1f + - 301e07345c93 + - c6ae57f774c6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: + - b7c3e9a3b954 + - 80852884053f - 4ed102b922cb - - 0630258dcf35 - 02d2be90dedb - f9639b488779 - - b7c3e9a3b954 - - 80852884053f + - 0630258dcf35 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: + - 14180f9c831e - caeb57858702 - 61634a87efc7 - - 14180f9c831e - ec69cbe34b73 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mapping.yml b/staging.gvl.org.au/mapping.yml index ff607abf7..f096df26c 100644 --- a/staging.gvl.org.au/mapping.yml +++ b/staging.gvl.org.au/mapping.yml @@ -3,16 +3,16 @@ tools: owner: devteam revisions: - f6877ad76b00 - - d5ceb9f3c25b - - 749c918495f7 - - cd659e8cc5fa - - a6d65b0c67af - - 03e9b2fbc005 - 0d4acadabb04 - - 937aa69e715f + - d5ceb9f3c25b - 17062a0decb7 + - a6d65b0c67af - 3ba8d4563129 + - 937aa69e715f + - 749c918495f7 - 017aba02828d + - 03e9b2fbc005 + - cd659e8cc5fa tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,18 +24,18 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - bfaa0d22c2e4 - b4a22d90cce9 + - bfaa0d22c2e4 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - e188dc7a68e6 - - 53646aaaafef - - 64f11cf59c6e - dfd8b7f78c37 + - 53646aaaafef - 2477830927ec + - 64f11cf59c6e - 3fe632431b68 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu @@ -48,46 +48,46 @@ tools: - name: lastz owner: devteam revisions: + - 2ff111fac1d7 - 37b497aa133f - - 3e1ea2facca6 - 60afcc2c1d05 + - 3e1ea2facca6 - e7f19d6a9af8 - - 2ff111fac1d7 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: minimap2 owner: iuc revisions: - - 53c0b7a1a0c3 - - 11a0d50a54e6 - - 09b53c1d4ab1 - - 3f4d6399997b - 6b1e195506a3 - - c0c2d0941de8 - - be1d967337e4 - - b3eab4b67562 - 037c6e54df11 - f54f5baedfdd - - 77b2770508f6 - - 8c6cd2650d1f - 5cc34c3f440d + - 8c6cd2650d1f + - 77b2770508f6 + - 53c0b7a1a0c3 + - be1d967337e4 + - 3f4d6399997b + - b3eab4b67562 + - 09b53c1d4ab1 + - 11a0d50a54e6 + - c0c2d0941de8 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: - - e403d27e8f24 - - 5ef7ec16b04f + - 42ce70172b72 - 00fbfac99d39 - 79b885ce78d7 - - 178bdbdb6d24 - - 13022c3d3076 - - ec9cbd6b9a49 - - 9ee34ba73ebf - 1cd2511a396e - - 42ce70172b72 + - 9ee34ba73ebf - 45795f582ae9 + - 178bdbdb6d24 + - 5ef7ec16b04f + - ec9cbd6b9a49 - b8f5f6e87f5c + - e403d27e8f24 + - 13022c3d3076 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/staging.gvl.org.au/metabolomics.yml b/staging.gvl.org.au/metabolomics.yml index ea13feabd..618d9d7cd 100644 --- a/staging.gvl.org.au/metabolomics.yml +++ b/staging.gvl.org.au/metabolomics.yml @@ -88,15 +88,15 @@ tools: - name: matchms_add_key owner: recetox revisions: - - 1d10d32fa3b3 - a5d41764722d + - 1d10d32fa3b3 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - 9e83636da9d3 + - b9cc12600553 - c990df6afc24 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,33 +111,33 @@ tools: - name: matchms_fingerprint_similarity owner: recetox revisions: - - 84af792d3a78 - - d7b517f2c5fe - fd890f162ce6 + - d7b517f2c5fe + - 84af792d3a78 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter owner: recetox revisions: - a5a5b147da70 - - 1b09315a3f87 - 9e3c83d2afc3 + - 1b09315a3f87 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_export owner: recetox revisions: - - f04610d25411 - b576ed720711 + - f04610d25411 - 8832425b1ff6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_match owner: recetox revisions: + - 330b0dfae8da - 1d443ed476a1 - 03bc9b7f40f6 - - 330b0dfae8da tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -158,15 +158,15 @@ tools: - name: matchms_remove_key owner: recetox revisions: - - fbdb2ae524df - 9d1b01d3fedd + - fbdb2ae524df tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_remove_spectra owner: recetox revisions: - - fbe335d27d25 - d50ce2f51fc0 + - fbe335d27d25 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_similarity @@ -178,17 +178,17 @@ tools: - name: matchms_spectral_similarity owner: recetox revisions: - - 7627b40601f6 - 9ff95a1a2705 - 7ba589b01dbc + - 7627b40601f6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_split owner: recetox revisions: + - 0cf68b536cd1 - 500f473df7e4 - ea6c5636c0cf - - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -270,57 +270,57 @@ tools: - name: recetox_aplcms_align_features owner: recetox revisions: - - c53a97599181 - 7b42ee54d757 - ec196e27a61a - 79ad928a0dae + - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - f3a18e020cdd + - 149b9cc7499b - 18ec7635bac6 - 59c393d35e0e - - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template owner: recetox revisions: - - 50b9918aeff2 - - 134be5abb208 - dfebc82ba1f0 + - 50b9918aeff2 - 481d769e2f7a + - 134be5abb208 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - 501a232f3cd5 - - 30bf4e35da3e - - a82db010c53e - 51332c2520c7 - - 9064aecc78a7 - 02c772a49998 + - 30bf4e35da3e + - 501a232f3cd5 + - 9064aecc78a7 + - a82db010c53e tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - b341cfd4baf8 - - e7305ba0dd38 - 89178a72388a - b3413f335327 + - b341cfd4baf8 + - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: + - cf061712a184 - b7c8a44b9cc1 - 17a48d0a80f4 - dd7bbc2b99d1 - - cf061712a184 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_recover_weaker_signals @@ -328,17 +328,17 @@ tools: revisions: - d7f5878a98c3 - f92b1b64da93 - - 24278c6b6d1c - 99d118321d5f + - 24278c6b6d1c tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_remove_noise owner: recetox revisions: - - ea0758b41473 + - 7acd11ddc061 - d90187b0f247 + - ea0758b41473 - ffbabefbd2e2 - - 7acd11ddc061 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_msfinder @@ -400,8 +400,8 @@ tools: - name: use_theoretical_mz_annotations owner: recetox revisions: - - e0cac9994a72 - b3d41b1fcb18 + - e0cac9994a72 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: w4mclassfilter diff --git a/staging.gvl.org.au/metagenomic_analysis.yml b/staging.gvl.org.au/metagenomic_analysis.yml index e1ef2be8f..91f9d36d6 100644 --- a/staging.gvl.org.au/metagenomic_analysis.yml +++ b/staging.gvl.org.au/metagenomic_analysis.yml @@ -8,9 +8,9 @@ tools: - name: cat_bins owner: iuc revisions: - - 0e63d03c8790 - 0094893f5001 - 18676df0cb3a + - 0e63d03c8790 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: cat_prepare @@ -22,8 +22,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - 7f1aaa1932d8 - a8216def322b + - 7f1aaa1932d8 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -96,70 +96,70 @@ tools: owner: iuc revisions: - 76d3d2b10738 - - 65db807336bc - - 7c2100246a2f - 5b5a7af9fbb4 - 63f86089423e + - 7c2100246a2f + - 65db807336bc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: + - 18a502a9d287 - 00f5005840fa - - 96336c6a2bb7 - 1c35dadbe76f - - 18a502a9d287 - 84fd33a60b35 + - 96336c6a2bb7 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_filterandtrim owner: iuc revisions: + - f732237754fc - addaf9d22850 - - 34e55239e68b - e8fba04706d3 + - 34e55239e68b - a9f4a217dcd6 - - f732237754fc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 5fe3edf19b9c - - 75403243703a - - 0776d824d896 - 04c15826a0b8 + - 5fe3edf19b9c - 8c202e741d68 + - 0776d824d896 + - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - 75c8945b0da2 - - 1c9b3bcd4261 - - 43c99742158b - e96bbb9e24ea + - 1c9b3bcd4261 - 8470de786d47 + - 43c99742158b + - 75c8945b0da2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 5c865a382933 - 306a40d4bb8f + - 35176674168c + - 5c865a382933 - 84743da21318 - 1d75bd0595e2 - - 35176674168c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotcomplexity owner: iuc revisions: - 555ccac8a4c5 + - 32c9ea835770 - 8daf4564ccda - - 78faebd0879c - ac72310b038a - - 32c9ea835770 + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile @@ -175,20 +175,20 @@ tools: - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e - - 7f3b59dee073 - 073608a50ac3 - - 1bc3657cd694 + - 7f3b59dee073 + - 04144473e59e - 7136e9ab70db + - 1bc3657cd694 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: + - 9058d8943303 - 0a1224c4b781 - d943081510da - 19299bb1c6af - - 9058d8943303 - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -202,28 +202,28 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - f8f56dd6449f - - 4d9445dff47b - - 65d52c693b8e - c4db8c4de66f + - 4d9445dff47b + - f8f56dd6449f - dbf1798c0dcc - - 5c7ba3d85a01 + - a68b985913ab - b907a3c0434f + - 5c7ba3d85a01 + - 65d52c693b8e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta owner: galaxy-australia revisions: - - 15dbb444df71 - 213df31ba341 + - 15dbb444df71 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_genefamilies_genus_level owner: iuc revisions: - - 654548ae1357 - 6c84982ee6f7 + - 654548ae1357 - 6d364c65c946 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -236,9 +236,9 @@ tools: - name: humann2_regroup_table owner: iuc revisions: - - 6aad8ca3918b - - e66ab198ec15 - bd7a9c6efb10 + - e66ab198ec15 + - 6aad8ca3918b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table @@ -253,8 +253,8 @@ tools: owner: iuc revisions: - 9704f1a3b32d - - cad93abecac9 - 7f208f1eb64f + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -272,54 +272,54 @@ tools: - name: humann_barplot owner: iuc revisions: - - 523ae8314ef5 - 5fea25ee6275 + - 523ae8314ef5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables owner: iuc revisions: - - 6bf703133209 - f01ca38fb6c5 + - 6bf703133209 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_reduce_table owner: iuc revisions: - - 60749924ad62 - 6552df6efe6b + - 60749924ad62 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_regroup_table owner: iuc revisions: + - 79706f10d680 + - c409a495841f - 31c6d107e7a5 - 8237a0f225db - - c409a495841f - e88b731dad59 - - 79706f10d680 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - 094ad9c068af - - d24841f5c3d2 + - aabf8cfb8fef - 71ea608ddfa3 - 172920f67a84 - - aabf8cfb8fef - 714d5a28cc5c + - d24841f5c3d2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - d7e9a3c41657 - - 4137b492233e - a293a742194f + - d7e9a3c41657 - 2bdd84912a2b - - a4d7148ccee4 + - 4137b492233e - 12fb63b5f63f + - a4d7148ccee4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -331,12 +331,12 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: - - cf87759761eb - - 75bedfb2078b - a92c06a3afa7 + - 75bedfb2078b + - cf87759761eb - 97f7bb0851e7 - - e2c71b852aba - 64bc7acc22a9 + - e2c71b852aba - 6fcb8ac37a3e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -356,12 +356,12 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: + - 5e5a999ffaa9 + - 2d35528d2141 - 080ea153677c - - c82508e76ad1 - - 4e5e73d03f0d - 4033827c76b8 - - 2d35528d2141 - - 5e5a999ffaa9 + - 4e5e73d03f0d + - c82508e76ad1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann @@ -389,15 +389,15 @@ tools: - name: jellyfish owner: iuc revisions: - - 11658afb8c87 - dcd30574a456 + - 11658afb8c87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution_single owner: iuc revisions: - - 385a965c6f87 - 65b382bf9b7c + - 385a965c6f87 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_abundance_distribution @@ -438,8 +438,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - b1fe2ef3d244 - 4d23ab83ea29 + - b1fe2ef3d244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -458,10 +458,10 @@ tools: - name: kraken2 owner: iuc revisions: - - cdee7158adf3 - - 20e2f64aa1fe - 4a9da2b6c2e3 - 328c607150ff + - cdee7158adf3 + - 20e2f64aa1fe tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax @@ -480,8 +480,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 5bee9adae474 - 67236d921e83 + - 5bee9adae474 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -507,8 +507,8 @@ tools: - name: kraken owner: devteam revisions: - - 8ba2174315aa - 766d5f63b0f4 + - 8ba2174315aa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -520,37 +520,37 @@ tools: - name: krakentools_beta_diversity owner: iuc revisions: - - c254d75b8b67 - 4505d7643673 + - c254d75b8b67 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_combine_kreports owner: iuc revisions: - - 073c867c5244 - 3d2cffa2c4ab + - 073c867c5244 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - - f329328da134 - 4bf1e2701504 + - f329328da134 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona owner: iuc revisions: + - 02bbace216f2 - 2deaada69b14 - 88d274322340 - - 02bbace216f2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2mpa owner: iuc revisions: - - bb96a1e6583d - d33cf727ed94 + - bb96a1e6583d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -580,22 +580,22 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: - - e073891b2afc + - 4fd3b5d8706b + - 327d9f4cc95f - 27250f92a01a - 2cff76cf35c6 - - 0270541aaf46 - - 327d9f4cc95f - - 4fd3b5d8706b - - 3cc4a60615c0 + - e073891b2afc - 7f5d7b0e9884 + - 3cc4a60615c0 + - 0270541aaf46 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metabat2 owner: iuc revisions: - 76bc4efa1aeb - - eb50e7eca3dc - 708abf08a626 + - eb50e7eca3dc tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -668,19 +668,19 @@ tools: - name: metaphlan owner: iuc revisions: - - ff8f55893e7d - - 6dee4abadccb - 2131d7dca455 - - 289b3807e80c + - ff8f55893e7d - b89b0765695d - - a92a632c4d9b + - ec368db926f4 - fd69c607b43f - - 1a6cdf55390f + - 289b3807e80c - a16313517e55 - - ec368db926f4 - - ef65b083bd0c - - 740fd2d16a28 - 1a037928504c + - 1a6cdf55390f + - a92a632c4d9b + - 740fd2d16a28 + - ef65b083bd0c + - 6dee4abadccb tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -696,6 +696,12 @@ tools: - 54897b7e0551 tool_panel_section_label: Metagenomic Analysis tool_shed_url: testtoolshed.g2.bx.psu.edu +- name: phyloseq_from_dada2 + owner: iuc + revisions: + - 40ebae5bbe51 + tool_panel_section_label: Metagenomic Analysis + tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_ordination_plot owner: simon-gladman revisions: @@ -719,8 +725,8 @@ tools: - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline @@ -733,8 +739,8 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs @@ -747,8 +753,8 @@ tools: - name: picrust2_shuffle_predictions owner: iuc revisions: - - 677f3c8db525 - 881f2faa5fe7 + - 677f3c8db525 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_categorize @@ -760,8 +766,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 8e2ac1b8f70a - 0ba7dfaa941d + - 8e2ac1b8f70a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -817,20 +823,20 @@ tools: - name: recentrifuge owner: iuc revisions: - - 591175c0f051 - d4fbfd31696c + - 591175c0f051 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - 141afacabcfa - - aeaa20b96ef2 - 4b9a8031ab74 - 2fd4d4c9c5c2 - 4d83eccf5f81 - 3b22de20bd4b - be818ae858e4 + - 141afacabcfa + - aeaa20b96ef2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: usearch_cluster_otus @@ -860,8 +866,8 @@ tools: - name: vsearch owner: iuc revisions: - - 576963db5f1b - b3c7199d8786 - 9495df9dd6ef + - 576963db5f1b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/mothur.yml b/staging.gvl.org.au/mothur.yml index 193493f23..63fd21d8b 100644 --- a/staging.gvl.org.au/mothur.yml +++ b/staging.gvl.org.au/mothur.yml @@ -652,8 +652,8 @@ tools: - name: mothur_screen_seqs owner: iuc revisions: - - f4d7d5755f01 - 63b74bfc8052 + - f4d7d5755f01 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_sens_spec @@ -707,8 +707,8 @@ tools: - name: mothur_sub_sample owner: iuc revisions: - - 67cb43432196 - e866e31f6da3 + - 67cb43432196 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_qual @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 72be09dfd803 - 2344ed181ae6 + - 72be09dfd803 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/staging.gvl.org.au/multiple_alignments.yml b/staging.gvl.org.au/multiple_alignments.yml index 8e7561434..9012b1e89 100644 --- a/staging.gvl.org.au/multiple_alignments.yml +++ b/staging.gvl.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - bdfbaf0c10aa - - a74dbfee5a86 - - 80f03df2e2ce - - 2263989660f5 - - cd07731e4434 - - 6ae5a7b5a0a2 - 098506c54016 - 9baa871cb1d1 - - 9422c5a87ee2 - 94b8c6013083 - - 9eeb13a92d79 + - 2263989660f5 + - 80f03df2e2ce - 48c13389050d + - cd07731e4434 + - bdfbaf0c10aa + - 6ae5a7b5a0a2 - 8b67dd48fec1 + - a74dbfee5a86 + - 9422c5a87ee2 + - 9eeb13a92d79 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - - f0af8936ed41 - - c18157c68134 - - 2e093badc689 - - fc2e49f91e52 + - aaa0d6a8b808 - 3ff17bad4006 - - 4a60927aaca5 + - f0af8936ed41 - be78f13134e2 - - d390fe1567dc - - aaa0d6a8b808 - '764845535798' + - 5abf2c2249aa - d7ce0ec78e51 - - c44f824c051a - bc3831dd65c1 + - d390fe1567dc - f14193ec1f50 - - 5abf2c2249aa + - c44f824c051a + - fc2e49f91e52 + - 4a60927aaca5 + - c18157c68134 + - 2e093badc689 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -67,13 +67,13 @@ tools: - name: mafft owner: rnateam revisions: + - 8e649f27aa0d + - 15974dd17515 + - 6f28e90db932 - f0d493f8f84f - - bf28a8cff401 - - a65296ffb4a0 - f1a5908ea2cb - - 6f28e90db932 - - 15974dd17515 - - 8e649f27aa0d + - a65296ffb4a0 + - bf28a8cff401 - c5908940967d tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu @@ -88,9 +88,9 @@ tools: - name: mummer_dnadiff owner: iuc revisions: - - 60698466facd - - c9685bc0407c - 5561a1193611 + - c9685bc0407c + - 60698466facd tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer @@ -112,16 +112,16 @@ tools: - name: mummer_nucmer owner: iuc revisions: - - e18267f90096 - 7cd7a55a678d + - e18267f90096 - 636b049e6141 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - b4124df98b26 - - 959c1f8dae95 - cf3c9489c088 + - 959c1f8dae95 + - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/nanopore.yml b/staging.gvl.org.au/nanopore.yml index d8ac29f47..3b17aceb2 100644 --- a/staging.gvl.org.au/nanopore.yml +++ b/staging.gvl.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 9aa9d92c3c51 - 18a8d140ec6f - 7c47b3c9e493 - 28928576e1ea + - 9aa9d92c3c51 - 1145758d2f0b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -24,10 +24,10 @@ tools: - name: dorado owner: galaxy-australia revisions: - - 63d8ecfcfab1 - - 090ab4f31074 - 6942f170cc43 - fc5b6491cf78 + - 63d8ecfcfab1 + - 090ab4f31074 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: guppy_basecaller @@ -40,20 +40,20 @@ tools: owner: iuc revisions: - fc8804320156 - - 79e9a869f40e - - 72b5e9dda577 - - cb34f00cc10f - a7228a7ea146 - 0e9e7fcdd543 + - cb34f00cc10f + - 79e9a869f40e + - 72b5e9dda577 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: + - db25ec99c3ea - 18505fe2bdb1 - d6cddc06aeae - fa11aa8103b2 - - db25ec99c3ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -66,14 +66,14 @@ tools: owner: iuc revisions: - 19f3b583a9b3 - - eb746fa6f514 - - ec699520444c - cc36773a3681 - 43815fa60f3a - - 2bf63b38ee9b - 0f5f4a208660 + - eb746fa6f514 - edf6d4003fad + - ec699520444c - 222669c4afb6 + - 2bf63b38ee9b tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -92,53 +92,53 @@ tools: - name: nanoplot owner: iuc revisions: - - a38bdcec9e4c - - edbb6c5028f5 - - 645159bcee2d - - 7b379e98b9a9 + - 0f1c34698076 - a02b8b3f5a0c - a3c4fe6f49ab - - 0f1c34698076 + - 645159bcee2d + - edbb6c5028f5 + - a38bdcec9e4c + - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - 3b6f94fc7e1d - - 85a394edc247 - d219b6d8158a + - 85a394edc247 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - 90a922f32523 - be95355fef8d + - 90a922f32523 - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - d376944466bf - - 449e9aeded2d - 4857d5bcce52 + - 449e9aeded2d + - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - bec636361cfd - - a3afc5f0a96c - de5b3d8f5b90 + - a3afc5f0a96c + - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: porechop owner: iuc revisions: + - 543cbeef3949 - 93d623d9979c - 5f76b20953e5 - - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -157,8 +157,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - d1805f9c4c82 - 47936349f3e9 + - d1805f9c4c82 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -190,8 +190,8 @@ tools: - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 26e6c9362b7b + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/staging.gvl.org.au/none.yml b/staging.gvl.org.au/none.yml index c4cc716b3..18896dfe2 100644 --- a/staging.gvl.org.au/none.yml +++ b/staging.gvl.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: annotation_profiler @@ -28,8 +28,8 @@ tools: - name: bcftools_plugin_frameshifts owner: iuc revisions: - - 58341ad4fb42 - 96d2000977ab + - 58341ad4fb42 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -59,19 +59,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: - - baceff842902 + - 3e73c97f025d + - d74850cf4e42 - 97b1b5ad1cda - adfd6bf710bd - - d74850cf4e42 - - 3e73c97f025d + - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: + - 1586b111d2a3 - 9dd107db92c2 - 83da94c0e4a6 - - 1586b111d2a3 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -83,11 +83,11 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - e9ee4d074d5d - - 2f27f3b86827 - - 1e34d2e3d285 - edacc4bcd3cb + - 1e34d2e3d285 - e4b4837f06f5 + - e9ee4d074d5d + - 2f27f3b86827 - ed1518ce2237 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -114,8 +114,8 @@ tools: - name: data_manager_dada2 owner: iuc revisions: - - 5711fc06a63e - 38ccd4589990 + - 5711fc06a63e - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -129,22 +129,22 @@ tools: - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco owner: iuc revisions: - - 2b4526fdf7fb - 15b97817550a + - 2b4526fdf7fb tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam revisions: - - 4d3eff1bc421 - b1bc53e9bbc5 + - 4d3eff1bc421 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_funannotate @@ -156,17 +156,17 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - 5bcf0e24f42c - - 172815da3d41 - b4b2b284230a - 27a6a256cd23 + - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gtdbtk_database_installer @@ -193,8 +193,8 @@ tools: owner: iuc revisions: - 87febc68b45b - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -207,8 +207,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 4c7ebbad42cf - 15c2fc266540 + - 4c7ebbad42cf tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -226,12 +226,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - 9c43baa60906 + - 5fe20c915fa6 - d8dc037e3c13 - - 0cb27ea69dc1 - 4ba60cb14cb0 + - 0cb27ea69dc1 - 2c61c30a57e7 - - 5fe20c915fa6 + - 9c43baa60906 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -245,17 +245,17 @@ tools: owner: iuc revisions: - 9d09724f2bf1 - - 0db22932bc39 - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - 29c738066906 - - 6e24e79d3d69 - ed7a967cb11b + - 6e24e79d3d69 + - df30a2f1db55 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -294,17 +294,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - c520a52b5174 - d63c1442407f + - c520a52b5174 - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: - - 625fd9476402 - - 9946bc39c834 - 94a50db37d1a + - 9946bc39c834 + - 625fd9476402 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -1068,9 +1068,9 @@ tools: - name: rdock_rbdock owner: bgruening revisions: + - e4b7d1507a75 - a22969b08177 - c362398df83b - - e4b7d1507a75 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -1082,11 +1082,11 @@ tools: - name: salsa owner: iuc revisions: - - ab5b7f6b7198 + - 9a22227bb6d0 + - f77f7a7f3b83 - 58a870ef434c - ba7b0f11e470 - - f77f7a7f3b83 - - 9a22227bb6d0 + - ab5b7f6b7198 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_merge diff --git a/staging.gvl.org.au/phylogenetics.yml b/staging.gvl.org.au/phylogenetics.yml index 56b173e9f..0b1a23a3e 100644 --- a/staging.gvl.org.au/phylogenetics.yml +++ b/staging.gvl.org.au/phylogenetics.yml @@ -26,8 +26,8 @@ tools: - name: gubbins owner: iuc revisions: - - 96e6283e4745 - 637ec5d5368c + - 96e6283e4745 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -39,66 +39,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: + - 5a7c56a5cc08 + - 3b8b5bde0bd9 + - 6a457678efcb + - 8834daeb9892 + - f73435dc282b + - d7c7ef3353fe + - 81e66674859e - a6619171428e - f04a1264e2a2 - - 81e66674859e - 107d3ba7024a - - 6a457678efcb - - 5a7c56a5cc08 - - f73435dc282b - '841557158611' - - d7c7ef3353fe - - 3b8b5bde0bd9 - - cce7b18495e4 - - 3f59ebfbfe3d - b89cac5156ec + - 3f59ebfbfe3d - d033ffc1c161 - - 8834daeb9892 - - 26de3a7b1cb9 + - cce7b18495e4 - c78f3d7dd1db + - 26de3a7b1cb9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 4755f52427c4 + - 6223845127ea + - 02b8758214b0 + - 88c4aa435ded + - 5b777002c2de - 5fcd1ece3a6e + - b0af57c1a968 - 659517798cc4 - - 5b777002c2de - - 02b8758214b0 - df47d4845b62 - - 6223845127ea - - b0af57c1a968 - 7a2092844346 - - a185b079b095 - 6a726db04d4b - aa8cc71438cf - - 88c4aa435ded - - 6283babe736e - - 4755f52427c4 + - a185b079b095 - 3b96e92e8ec3 + - 6283babe736e - e75442c7f4da tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - b8476e82ac20 - - d1c340a5664b - - 24d024316465 - f97743d52b87 - 70acec670c30 + - f87ac61981f0 + - 24d024316465 + - b8476e82ac20 - 524d31add34a + - d1c340a5664b - 111bd54f6bc4 - - f87ac61981f0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - 4f6349228462 - - feb40665d7cd - - 9e10ba792be2 - daddf188c13f + - 9e10ba792be2 + - feb40665d7cd + - 4f6349228462 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -110,33 +110,33 @@ tools: - name: pangolin owner: iuc revisions: - - ca337cce3888 - - 81804a978fc0 - - a2099fb98cdb - - 42a174224817 - - 14ae456b8cc5 - - 03ed9524dcd1 + - ca0d8cf80567 + - 83a69484cb87 - 5f8727ff21e7 + - 9d61d3fa046c + - 81804a978fc0 + - b7e297c2ede6 - 2f1019071464 + - a2099fb98cdb - abf6dbe8c9d7 - - 83a69484cb87 - 2fa9d4f1b48f - - b7e297c2ede6 - - 9d61d3fa046c - - ca0d8cf80567 - - 8ad84c5753ea + - 437e28791761 - 36912871ccdc + - 14ae456b8cc5 + - b6abccb1f25b + - 42a174224817 - 3a43c3982401 - - 437e28791761 + - ca337cce3888 - 7bb8726be37c - - b6abccb1f25b + - 8ad84c5753ea + - 03ed9524dcd1 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml owner: iuc revisions: - - 7157a5b34a68 - 2bf47d57ebb5 + - 7157a5b34a68 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: rapidnj @@ -150,21 +150,21 @@ tools: revisions: - 29ff6a849eac - 73a469f7dc96 - - a4b71be30c3c - ea30d3089354 - - ba29b5e2a4be + - a4b71be30c3c - b1e68bbe4cef + - ba29b5e2a4be tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 - - dbe2b2204555 - - e88a7de55d6e - f1ccc8a6eb05 + - 15ac71df11a0 + - 91887494eb97 - 809e42326fc2 + - e88a7de55d6e + - dbe2b2204555 - 9b2b122d0415 - - 15ac71df11a0 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/picard.yml b/staging.gvl.org.au/picard.yml index 56126436e..9362d244a 100644 --- a/staging.gvl.org.au/picard.yml +++ b/staging.gvl.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: + - f9242e01365a - 3f254c5ced1d + - fc288950c3b7 + - 881d7645d1bf + - 7d34178f2812 - 1aac2a13842a - f6ced08779c4 - a1f0b3f4b781 - - fc288950c3b7 - - 7d34178f2812 - - f9242e01365a - b502c227b5e6 - - 881d7645d1bf tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomic_ai.yml b/staging.gvl.org.au/proteomic_ai.yml index 3116cefae..8905b4dcc 100644 --- a/staging.gvl.org.au/proteomic_ai.yml +++ b/staging.gvl.org.au/proteomic_ai.yml @@ -2,18 +2,18 @@ tools: - name: alphafold2 owner: galaxy-australia revisions: - - a58f7eb0df2c - - 3bd420ec162d - - e4a053d67e24 - - e7f1b552a695 - - eb085b3dbaf8 - - 5b85006245f3 - 7fbec959cf2b + - ca90d17ff51b + - 5b85006245f3 + - eb085b3dbaf8 + - e7f1b552a695 - 6ab1a261520a - 2f7702fd0a4c + - d00e15139065 - c0e71cb2bd1b - - ca90d17ff51b - 3f188450ca4f - - d00e15139065 + - 3bd420ec162d + - e4a053d67e24 + - a58f7eb0df2c tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/proteomics.yml b/staging.gvl.org.au/proteomics.yml index 99a842d5a..d3760e343 100644 --- a/staging.gvl.org.au/proteomics.yml +++ b/staging.gvl.org.au/proteomics.yml @@ -2,24 +2,24 @@ tools: - name: cardinal_classification owner: galaxyp revisions: - - 0a18ac48ac53 - - b574b84afc4d - - ece627528a78 - - 4c177985028a - 277dc652246e - - f28ad96b76dc + - 4c177985028a - b18329a8ac14 + - 0a18ac48ac53 + - f28ad96b76dc + - ece627528a78 + - b574b84afc4d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - e215f71d7983 + - a9a28e46d54a - 525f201b86c1 - bf06d196e23d - b41107d8fe89 + - e215f71d7983 - e988563cc6e5 - - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter @@ -37,59 +37,59 @@ tools: - b8c79e70516d - f23d67e28cc8 - 528fb09022be - - a8157342d9a3 - 890845926d4b + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - 25b83cbd596a - - 80600735685d - - a69865da6f80 - - ae304a72db7b - 59e85306eae5 + - ae304a72db7b - a95a82eb4d50 + - 80600735685d + - 25b83cbd596a + - a69865da6f80 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 798da6bdff3d - - 611d80c0e29d - ed9ed1e6cca2 - - e0669b1854b1 - - 83aac7741200 - f1897eb07081 + - 83aac7741200 + - e0669b1854b1 + - 611d80c0e29d + - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - d426a9107a6c - 5a35e3a8d013 - a7fb9b395ddf + - d426a9107a6c - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - cc430977c8ff - - df2187f9013b - 82f6c2f4332d - 91f0f5922011 + - df2187f9013b + - cc430977c8ff tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_spectra_plots owner: galaxyp revisions: - ba92b59cd529 + - c5aa9fca18c6 + - 043f9c91f686 - 10566783d718 - d2483487e077 - - 043f9c91f686 - 1693b2126f30 - - c5aa9fca18c6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: custom_pro_db @@ -109,8 +109,8 @@ tools: revisions: - bf0728e000cd - 9fa3dbf06f17 - - ae4dc0c041f9 - ff8c9e0e8a7b + - ae4dc0c041f9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -129,24 +129,24 @@ tools: - name: encyclopedia_quantify owner: galaxyp revisions: + - 4081e4faa4ab - 0fa397f4f40b - 1c5cbf8f79ce - - 4081e4faa4ab tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - 36880dfd9fa7 - fb192dd6658a + - 36880dfd9fa7 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: + - 0d2e93e01e68 - d6a4dfdad269 - ce1a157a41bd - - 0d2e93e01e68 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -173,23 +173,23 @@ tools: - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 4d17fcdeb8ff - - 1f39c833f65f - - f522c08e900c - 9c52362ae7bb - - 2133b0be850a - - 837224ad1694 - 7f432d87c82c + - 4d17fcdeb8ff + - 837224ad1694 - 37d669de2828 - - 97a7f34fcb6a - e42225f8a659 + - 97a7f34fcb6a + - 1f39c833f65f + - f522c08e900c + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -202,77 +202,77 @@ tools: owner: galaxyp revisions: - 85b8866f06d7 + - 0ed07016d668 - a72ac2c7cc5b - e63db1aa82ee - - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_expand owner: galaxyp revisions: - - 767c1d761aaf - 990b4560ead7 - 1974224d63c2 + - 767c1d761aaf - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - 35cc7ca0bdc7 - 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c1809c05ae8c - 1bf940c18d93 - - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: - 9f505cd4428f - - f861ec9fbe59 - 496cf619e311 + - f861ec9fbe59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: - - c99d5004b74f - - 0bddef8d144e - d4396637b9f5 + - 0bddef8d144e + - c99d5004b74f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - 8b814eafce2c - 4bb198c0bd3e + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: - 05ec9fb05ed1 - - f9ed7e074900 - f82b320ceb90 + - f9ed7e074900 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: + - 6e8cc5ed2a9b - d31426ef20f6 - 18826fb8e5db - - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow @@ -536,60 +536,60 @@ tools: - name: openms_peakpickerhires owner: galaxyp revisions: - - decc397c3b7e - - 5ae104d0da6e - 3d8d4ada5405 - 6b01678ec2fc + - decc397c3b7e + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - 539a3a4dcc9e - - dd173849c3d8 - e039cc5c7aed - - d6aca689dd48 - 5182338d5e7c + - d6aca689dd48 + - dd173849c3d8 + - 539a3a4dcc9e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier owner: galaxyp revisions: - - 16026cdb1330 - 8a45fd5a608a - d426affe977c + - 16026cdb1330 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_targetedfileconverter owner: galaxyp revisions: - - dd71e020e2aa - 9c70a651a53e - 43b9ed22e8ce + - dd71e020e2aa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_textexporter owner: galaxyp revisions: - - d063e2fe4ba4 - 9020199dba0a + - d063e2fe4ba4 - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - f036e8cf1a55 - - ad2ba3a95a02 - 78c080d36945 + - ad2ba3a95a02 + - f036e8cf1a55 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter owner: galaxyp revisions: - c8b225c69a7f - - 5c2a97a234d6 - 7f6a1f27553e + - 5c2a97a234d6 - fb52e95a370c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -609,21 +609,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - 5f49ffce52cb - cb0378d2d487 + - 5f49ffce52cb tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 7fdd9119cc4f - - 3634c90301af - - 3ec27b4cee7c + - a72c48001f7c - 07ff622ec007 + - 3ec27b4cee7c + - 3634c90301af + - 7fdd9119cc4f - 1beff3ddce58 - - da885ca16cb2 - - a72c48001f7c - 943a34df6047 + - da885ca16cb2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -683,10 +683,10 @@ tools: - name: uniprotxml_downloader owner: galaxyp revisions: - - 265c35540faa - - 12692567c7f9 - 1a5690a5eedc + - 12692567c7f9 - a371252a2cf6 + - 265c35540faa tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/staging.gvl.org.au/rad_seq.yml b/staging.gvl.org.au/rad_seq.yml index e37ccd9e1..f7de839fc 100644 --- a/staging.gvl.org.au/rad_seq.yml +++ b/staging.gvl.org.au/rad_seq.yml @@ -2,12 +2,12 @@ tools: - name: stacks2_clonefilter owner: iuc revisions: + - cd5f98911089 + - 110a346daf36 - 289b7d6b69a4 + - 42201b90e3f4 - 2f1d464ebfd2 - e345aadf914f - - 110a346daf36 - - 42201b90e3f4 - - cd5f98911089 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_clonefilter @@ -19,12 +19,12 @@ tools: - name: stacks2_cstacks owner: iuc revisions: - - 0345dbaaa79b - - fcce77c09289 - 42d9087b4789 - 8501601a118d - - 0cd2df8af811 - c207119ba5f6 + - 0cd2df8af811 + - fcce77c09289 + - 0345dbaaa79b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_cstacks @@ -36,12 +36,12 @@ tools: - name: stacks2_denovomap owner: iuc revisions: + - 405a212b32ab - 04db7fd6b238 - 421c33b8bf17 - 33486216eec0 - - 405a212b32ab - - 89eb29319bf4 - ad5ab22ffe24 + - 89eb29319bf4 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_denovomap @@ -53,12 +53,12 @@ tools: - name: stacks2_gstacks owner: iuc revisions: - - f6e91108b7b1 - - fa51dc5e8386 - - 7b72fde3d27e - - 7370bb65bad4 - 1d839ead7ad3 - eb784fa07f80 + - 7370bb65bad4 + - f6e91108b7b1 + - 7b72fde3d27e + - fa51dc5e8386 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_gstacks @@ -70,12 +70,12 @@ tools: - name: stacks2_kmerfilter owner: iuc revisions: - - 8a55d29c8fcf - - d30e36c48c93 - 3d70c2996730 - 1544278c272e - - c9b77ced9a78 + - 8a55d29c8fcf - a3e86cd9cac7 + - d30e36c48c93 + - c9b77ced9a78 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_kmerfilter @@ -87,12 +87,12 @@ tools: - name: stacks2_populations owner: iuc revisions: - - b242deb58952 - - 887cf585cafc - - a5969aa9347e - e2db212d64ad - - 7b881f5f5ad5 + - 887cf585cafc - 564c33e5c3e3 + - 7b881f5f5ad5 + - b242deb58952 + - a5969aa9347e tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_populations @@ -105,8 +105,8 @@ tools: owner: iuc revisions: - e897c74a48bb - - b4bab607eb05 - bd5ff77e2036 + - b4bab607eb05 - 8cff84759bf6 - 9a171f9a450b tool_panel_section_label: RAD-seq @@ -120,12 +120,12 @@ tools: - name: stacks2_refmap owner: iuc revisions: - - adc7a7610d4f - - 4f65e343ecdf - - 5e10f396979e - - 887e0991eb24 - 6dafad990086 - 33f0793edf93 + - 887e0991eb24 + - adc7a7610d4f + - 5e10f396979e + - 4f65e343ecdf tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_refmap @@ -137,12 +137,12 @@ tools: - name: stacks2_shortreads owner: iuc revisions: - - 17d39bf0a63a - - 43e3eeb2e0ec - - c5d7050e4ad7 + - c287418eb288 - 4e280b27a831 + - c5d7050e4ad7 - 97575d01f06b - - c287418eb288 + - 17d39bf0a63a + - 43e3eeb2e0ec tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_shortreads @@ -154,12 +154,12 @@ tools: - name: stacks2_sstacks owner: iuc revisions: + - a819ec3b362d - 0b8c84a7fdb5 + - d9bf483266a1 - cd034465d4a4 - - a819ec3b362d - 9586f08634c0 - 09b8edb56d80 - - d9bf483266a1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks @@ -171,12 +171,12 @@ tools: - name: stacks2_tsv2bam owner: iuc revisions: + - 2645575d1bf2 - a9c34a289493 - - 69842dd5aa48 - - 95351dd0fd3f - a4b4bd84f69e - - 2645575d1bf2 - bf0e43ab0416 + - 95351dd0fd3f + - 69842dd5aa48 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam @@ -188,12 +188,12 @@ tools: - name: stacks2_ustacks owner: iuc revisions: - - d033e1ccb386 - - cfb504394ae1 - bb0475c884ff - - 8a35a3bc6752 - 912f904a6e1e + - d033e1ccb386 - d1fda11e602f + - 8a35a3bc6752 + - cfb504394ae1 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks @@ -236,8 +236,8 @@ tools: owner: iuc revisions: - d504d945a655 - - 95286af4139b - d1fad35bdb4a + - 95286af4139b tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_procrad diff --git a/staging.gvl.org.au/rna_seq.yml b/staging.gvl.org.au/rna_seq.yml index bd9946b8c..edfd9a1ab 100644 --- a/staging.gvl.org.au/rna_seq.yml +++ b/staging.gvl.org.au/rna_seq.yml @@ -2,27 +2,27 @@ tools: - name: arriba_draw_fusions owner: iuc revisions: + - 7acb00fc980a - cf01dd6c6b1f - - 2d4e3aff9dc7 - 31f8063eedea - - 7acb00fc980a + - 2d4e3aff9dc7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 32e542c2a773 - - 703a2cb3fb38 - 125d20cb23d7 - 7a5a2d28c539 + - 703a2cb3fb38 + - 32e542c2a773 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba owner: iuc revisions: - - 3d61a698e5e1 - 01ccd366690d - 45c2ec061cf9 + - 3d61a698e5e1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: blockbuster @@ -77,9 +77,9 @@ tools: - name: cuffcompare owner: devteam revisions: - - ad5d061fbdf2 - - e66b9b5b8580 - f648e5180e40 + - e66b9b5b8580 + - ad5d061fbdf2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffcompare @@ -91,8 +91,8 @@ tools: - name: cufflinks owner: devteam revisions: - - d080005cffe1 - 6926716bbfb5 + - d080005cffe1 - e04dbae2abe0 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -106,10 +106,10 @@ tools: owner: devteam revisions: - 86285ddd4512 - - 6a6717a5f421 - - 22cf48ad7b16 - cf747d1bd79a - 04adc9db1581 + - 22cf48ad7b16 + - 6a6717a5f421 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge @@ -121,9 +121,9 @@ tools: - name: cuffnorm owner: devteam revisions: + - 6cbfede05833 - 28b94cfbfdb9 - 9a854107dbb2 - - 6cbfede05833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm @@ -160,10 +160,10 @@ tools: - name: describe_samples owner: iuc revisions: - - 3b36efd62b3e - - 8f0181aacb7a - - e3b16fd7dd08 - 0693ccd171c4 + - e3b16fd7dd08 + - 8f0181aacb7a + - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: describe_samples @@ -175,13 +175,13 @@ tools: - name: deseq2 owner: iuc revisions: - - 9a882d108833 - d027d1f4984e - - cd9874cb9019 - 8fe98f7094de + - 6a3a025714d3 - 0696db066a5b + - cd9874cb9019 - 24a09ca67621 - - 6a3a025714d3 + - 9a882d108833 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 @@ -193,11 +193,11 @@ tools: - name: dexseq owner: iuc revisions: - - 9a7c5b6d8f1e - - df929f257179 - b47c006d90c5 - 2872c633f07e + - 9a7c5b6d8f1e - 62adf13b86ea + - df929f257179 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq @@ -209,18 +209,18 @@ tools: - name: edger owner: iuc revisions: - - f2843df56434 + - 6e53e565fc6a + - 9bdff28ae1b1 + - 555659de7321 + - 334ce9b1bac5 - 3d89af8a44f0 + - 5bf899c13979 + - f2843df56434 - ae2aad0a6d50 - - 334ce9b1bac5 - - 555659de7321 - - 070900306913 - a8305cf0c951 - - df0c8d0a5992 - 0cb907a2a810 - - 5bf899c13979 - - 6e53e565fc6a - - 9bdff28ae1b1 + - 070900306913 + - df0c8d0a5992 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger @@ -232,8 +232,8 @@ tools: - name: egsea owner: iuc revisions: - - 31ea4992b948 - fba1660fb717 + - 31ea4992b948 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea @@ -251,18 +251,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 1b851f87fbe0 - - f3a5f075498f - - f9d49f5cb597 - a56fbe2d6ba7 - - ea04b737afa0 - - 38b6d12edc68 + - 6f66ae7c5f7a - e6a2a912677a + - 38b6d12edc68 - 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name: htseq_count @@ -356,11 +356,11 @@ tools: - name: kallisto_pseudo owner: iuc revisions: - - 01247aaf0a10 - 5ae5c312d718 - - 1c75aa5de15e - - ce5d418183c5 + - 01247aaf0a10 - 87c11c05d238 + - ce5d418183c5 + - 1c75aa5de15e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_pseudo @@ -372,9 +372,9 @@ tools: - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - 4f9c4e6566e5 - 10c98fab6c5a + - c971db6f0fe5 - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -387,13 +387,13 @@ tools: - name: limma_voom owner: iuc revisions: - - e827f9aae031 - - 58c35179ebf0 - 32511f586472 - 97e06a4c7c75 - - d6f5fa4ee473 - - 0921444c832d - 708348a17fa1 + - 58c35179ebf0 + - e827f9aae031 + - 0921444c832d + - d6f5fa4ee473 - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -443,8 +443,8 @@ tools: - name: qualimap_counts owner: iuc revisions: - - 72927fc9e9ed - d696cf0a9622 + - 72927fc9e9ed tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_rnaseq @@ -462,21 +462,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 980d2a2e1180 + - b0f2be869d6d + - e132e7d02a3e + - 99b17b74a8cd + - 5ec75f5dae3c - 4074fc1940e2 - b9e04854e2bb - - 4df95e2d7f61 - - c772497b2c32 - - 79de45b5069b - - 5ec75f5dae3c - - b0f2be869d6d - c7c55b694974 - - 7ed2edc1337f + - 3ea5a2a63fa2 - 4014de1b6daf + - 7ed2edc1337f - 0a563fd2f22e - - 3ea5a2a63fa2 - - 99b17b74a8cd - - e132e7d02a3e + - 980d2a2e1180 + - c772497b2c32 + - 4df95e2d7f61 + - 79de45b5069b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rgrnastar @@ -500,14 +500,14 @@ tools: - name: salmon owner: bgruening revisions: - - cc05793bb896 - - 15cd64d7c58b - - 49121db48873 - - e3d32471da11 - ebab418107f5 - - f4d5237a84f6 - - 53e9709776a0 - 2c0ca397d302 + - 53e9709776a0 + - f4d5237a84f6 + - 15cd64d7c58b + - cc05793bb896 + - e3d32471da11 + - 49121db48873 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: salmon @@ -519,23 +519,23 @@ tools: - name: seurat owner: iuc revisions: - - 8c28affc7c48 - - fab6ff46e019 - 56242ff81c84 + - fab6ff46e019 + - 8c28affc7c48 - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - cef79931dda5 - - 1ebd14235b92 - - 914cfcba0ec8 - - dd4df992d93d - ae618321f34a - - 76d290331481 - - 258d696dbd7e + - dd4df992d93d - cbf488da3b2c + - 914cfcba0ec8 + - 258d696dbd7e + - 1ebd14235b92 + - 76d290331481 + - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie @@ -571,10 +571,10 @@ tools: - name: transdecoder owner: iuc revisions: - - 0db979fead3a - - d0d4cef4f967 - - ffd1300599a1 - c6334cb383ff + - ffd1300599a1 + - d0d4cef4f967 + - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: transdecoder @@ -586,10 +586,10 @@ tools: - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - - bcc5f03f1900 - - d6a479fd4281 - 74217fbfba4d - ba3720d7e68b + - d6a479fd4281 + - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix @@ -602,9 +602,9 @@ tools: owner: iuc revisions: - 2fb4ee002432 + - c2b82a94493e - 478f36effca1 - 56162e446004 - - c2b82a94493e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance @@ -630,10 +630,10 @@ tools: - name: trinity_contig_exn50_statistic owner: iuc revisions: - - 34a018cbee9c - be3f26533209 - 870ac06dff8e - 4687ecf0eb2d + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic @@ -645,11 +645,11 @@ tools: - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - - c5fbddcac63a - 5192f657f305 + - c5fbddcac63a - 65e7dea767ea - - 05ab8d5e04a2 - 33406f5a445c + - 05ab8d5e04a2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree @@ -662,8 +662,8 @@ tools: owner: iuc revisions: - a35cba31d904 - - 6f0fb35b799c - 1fdb25a8384d + - 6f0fb35b799c - e406ac71165d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -676,10 +676,10 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: + - 7c7fbf13aadd - c2c039e421af - - 37a1129c89d2 - 964b7efe2639 - - 7c7fbf13aadd + - 37a1129c89d2 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_gene_to_trans_map @@ -691,10 +691,10 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: - - 1d689e4e1caf - 047c22569787 - - 24e94d84adc9 + - 1d689e4e1caf - eafea3083352 + - 24e94d84adc9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_run_de_analysis @@ -708,8 +708,8 @@ tools: revisions: - 3a4ac03d1266 - 9871104ea630 - - 04bb8bb7c198 - 1812dbc5bb7b + - 04bb8bb7c198 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck @@ -733,15 +733,15 @@ tools: - name: trinity owner: iuc revisions: - - d2bc35f3d1c5 - c9cfec002f71 - - d84caa5a98ad - - cee61b3fcf78 - - 9fa24d5aac68 - 48636f857c4b - - 32b86cd8eb50 - - 8f1c3df4dd49 - db1f362cca3e + - cee61b3fcf78 + - d84caa5a98ad + - 8f1c3df4dd49 + - 32b86cd8eb50 + - 9fa24d5aac68 + - d2bc35f3d1c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity @@ -754,8 +754,8 @@ tools: owner: iuc revisions: - 4383070d29ed - - 6fd16fad465d - 2b093007fab9 + - 6fd16fad465d - 9e61bc67866f tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/rseqc.yml b/staging.gvl.org.au/rseqc.yml index 13cadf889..636b5a8af 100644 --- a/staging.gvl.org.au/rseqc.yml +++ b/staging.gvl.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: + - 27e16a30667a - 080fd5739bb4 - 1a052c827e88 - - 27e16a30667a - 473382134e56 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/sambam.yml b/staging.gvl.org.au/sambam.yml index 04dd20584..4173f5b9f 100644 --- a/staging.gvl.org.au/sambam.yml +++ b/staging.gvl.org.au/sambam.yml @@ -2,9 +2,9 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 10184eaa85fc - 88eedb4abea0 - 3c661e57a88f + - 10184eaa85fc tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bam_to_sam @@ -16,10 +16,10 @@ tools: - name: bamtools_filter owner: devteam revisions: - - 108db6635177 + - 1dfd95ee241e - cb20f99fd45b + - 108db6635177 - 993b19f20c76 - - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter @@ -63,8 +63,8 @@ tools: - name: pileup_interval owner: devteam revisions: - - ef11139d4545 - 9c1c0b947e46 + - ef11139d4545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: pileup_interval @@ -82,10 +82,10 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - 5f8e69cc4c6e - - 19ece8afbaab - 30a201c9c310 + - 19ece8afbaab - e7fd6754d093 + - 5f8e69cc4c6e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_bamqc @@ -110,8 +110,8 @@ tools: - name: sam2interval owner: devteam revisions: - - 8c737b8ddc45 - 75557c0908a9 + - 8c737b8ddc45 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_bitwise_flag_filter @@ -130,8 +130,8 @@ tools: - name: sam_to_bam owner: devteam revisions: - - 0e60e2dd20af - cf1ffd88f895 + - 0e60e2dd20af tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam_to_bam @@ -150,8 +150,8 @@ tools: owner: devteam revisions: - 56c31114ad4a - - 649a225999a5 - dc6ff68ea5e8 + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip @@ -163,10 +163,10 @@ tools: - name: samtools_bedcov owner: devteam revisions: - - 6856f8a01905 - 46c6639921f1 - - 12749212f61b - 9149ad20699a + - 12749212f61b + - 6856f8a01905 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov @@ -178,10 +178,10 @@ tools: - name: samtools_calmd owner: devteam revisions: - - 33208952b99d - - 92ec40abcdcf - 06dc50b7b711 + - 33208952b99d - 26b4f9f98aca + - 92ec40abcdcf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd @@ -206,10 +206,10 @@ tools: owner: iuc revisions: - a8d69aee190e - - 720217c23995 - - b906586a6596 - b3d99709fe1a - 66e23b11feae + - 720217c23995 + - b906586a6596 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fastx @@ -221,18 +221,18 @@ tools: - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: + - fe34990e5ce7 - db17d5321bad + - cc61ade70eb8 - 22970df7a40e - - fe34990e5ce7 - fefd89ab563c - - cc61ade70eb8 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat @@ -244,10 +244,10 @@ tools: - name: samtools_idxstats owner: devteam revisions: - - 811fc2d75ad4 - - 7def34e6cf4d - fa5d3e61e429 - 7a6034296ae9 + - 7def34e6cf4d + - 811fc2d75ad4 - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -260,28 +260,28 @@ tools: - name: samtools_markdup owner: iuc revisions: - - 40fa6c240105 - a389f74c3630 + - 40fa6c240105 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_merge owner: iuc revisions: - - b40e2d865d52 - 65a38e8c8e2a - 740ce0a18f0d - - 36677f429310 + - b40e2d865d52 - cae2794d2deb + - 36677f429310 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup owner: devteam revisions: - 329deb17a9f7 - - fa7ad9b89f4a + - b61f5d6a7f25 - 583abf29fc8e - 9da0311ab1dd - - b61f5d6a7f25 + - fa7ad9b89f4a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_mpileup @@ -306,10 +306,10 @@ tools: - name: samtools_reheader owner: devteam revisions: + - bb8cfc6f6e0c + - db000c6007a0 - 85e38b31e8b3 - 30388d878f81 - - db000c6007a0 - - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader @@ -328,8 +328,8 @@ tools: owner: devteam revisions: - b8beef827165 - - 344fc91e1bfd - a4a10c7924d1 + - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_slice_bam @@ -341,10 +341,10 @@ tools: - name: samtools_sort owner: devteam revisions: - - 6c2c1836728b + - e613c1ad4c4c - cab3f8d35989 + - 6c2c1836728b - d54a4df48867 - - e613c1ad4c4c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort @@ -356,12 +356,12 @@ tools: - name: samtools_split owner: devteam revisions: - - 818030fa6bbf - - b7f7826ef1cd - bcedabb53ddf - - bd850490c7f1 - 5d9ae78f34d3 - 135c85f4cfaf + - b7f7826ef1cd + - bd850490c7f1 + - 818030fa6bbf tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split @@ -373,12 +373,12 @@ tools: - name: samtools_stats owner: devteam revisions: - - 541082d03bef + - 5a08c09b9311 - 145f6d74ff5e + - 541082d03bef - 1cc79f49b8d5 - - 24c5d43cb545 - - 5a08c09b9311 - 3a0efe14891f + - 24c5d43cb545 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats @@ -390,16 +390,16 @@ tools: - name: samtools_view owner: iuc revisions: - - b01db2684fa5 - - 32dc5f781059 - 6be888be75f9 - - 5826298f6a73 - - 0dbf49c414ae - - b72793637686 - - bf328cec6a42 - - c370440f901e + - 32dc5f781059 - 350bbc5c2ffd + - 0dbf49c414ae + - b01db2684fa5 + - 5826298f6a73 - 2dce91e11ca7 + - c370440f901e + - bf328cec6a42 + - b72793637686 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view diff --git a/staging.gvl.org.au/send_data.yml b/staging.gvl.org.au/send_data.yml index 2ebe2c208..8788e4f91 100644 --- a/staging.gvl.org.au/send_data.yml +++ b/staging.gvl.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - a62c4a11a67d + - 6f6537780379 - ea5e944f447d - - 5cb6146337d8 - - 480d9e9d156b - d147d6455873 - 4aab5ae907b6 - - 6f6537780379 + - 480d9e9d156b - 59bb6d34fca6 + - a62c4a11a67d + - 5cb6146337d8 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/single_cell.yml b/staging.gvl.org.au/single_cell.yml index 799a6b31e..de096f8c1 100644 --- a/staging.gvl.org.au/single_cell.yml +++ b/staging.gvl.org.au/single_cell.yml @@ -8,11 +8,11 @@ tools: - name: alevin owner: bgruening revisions: - - c9944a2600f1 + - b0fe3e482cb7 - ecb9ea6269ee - e32b215b7c04 + - c9944a2600f1 - f2000bc73102 - - b0fe3e482cb7 - e4c01dcece8b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -20,21 +20,21 @@ tools: owner: iuc revisions: - 7a6655aa6eb2 - - e1c3c2f2a834 - - c0b037b12765 - 707023fa62fe + - c0b037b12765 + - e1c3c2f2a834 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 6f143dfe902a - - 55e35e9203cf - - cfc3f5a57dc6 + - fb9e030ffae4 - 00712416fdaa - - 93dd15e13e6a - 32e547223c9e - - fb9e030ffae4 + - cfc3f5a57dc6 + - 93dd15e13e6a + - 6f143dfe902a + - 55e35e9203cf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import @@ -47,12 +47,12 @@ tools: owner: iuc revisions: - b9fac48532eb + - 688357ad5e61 - 14c576ea6148 - - 6f0d0c784f09 - 038e32885fec - - 688357ad5e61 - ee98d611afc6 - 39e945f0b2c1 + - 6f0d0c784f09 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect @@ -64,13 +64,13 @@ tools: - name: anndata_manipulate owner: iuc revisions: - - 9bd945a03d7b - b85871dd69f9 - c4209ea387d4 - - 43cb7b5a6fe7 + - 9bd945a03d7b - ed4996a16f7f - - 3d748954434b - d4af736e7b83 + - 43cb7b5a6fe7 + - 3d748954434b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate @@ -82,45 +82,45 @@ tools: - name: anndata_ops owner: ebi-gxa revisions: + - fe75d2414dc0 - 2e8022f1923c - a4774b7b2e85 - - fe75d2414dc0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_1d owner: iuc revisions: - - 0e70b2dfe4be - 4fff5a293013 - - 769d815e4b0d - 02b1fe7aed76 + - 769d815e4b0d + - 0e70b2dfe4be tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - c29e7bb492bf - 344c2af50552 - a90f8efe08b4 - aa4a6f0916b4 - - c29e7bb492bf tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: + - c32347702e12 - b13d3e4c48e1 - 5b7c81b35b89 - 050cf43887d3 - - c32347702e12 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - 239193b96d72 - 1d77986f9ddc - 02fc39c8610d - ae969fdb8442 + - 239193b96d72 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -156,10 +156,10 @@ tools: - name: dropletutils owner: iuc revisions: - - cfe1e6c28d95 + - 8855361fcfc5 - 2c1200fba922 + - cfe1e6c28d95 - cdf4443d5625 - - 8855361fcfc5 - a9caad671439 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -204,9 +204,9 @@ tools: - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: - - 57aeaf6b237d - - 9d42a6133690 - f1c35f3f310d + - 9d42a6133690 + - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata @@ -220,65 +220,65 @@ tools: - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - 013e53ccc7ac - f47ac4a0b337 + - 013e53ccc7ac - b9ab56aecd18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol owner: bgruening revisions: - - a63e9713c39d - 9ea228a9afc8 + - a63e9713c39d - b892fa1fcaec tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - f8320df1866b - 640e0e45518a + - f8320df1866b - 45a386d18509 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - 9d02f1819e81 + - f963c251ac77 - c354255ff705 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpoint owner: bgruening revisions: - - f881c94fb3b3 - c4ed35f4f77f - 40fee49bc6c3 + - f881c94fb3b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - 782bdcb775fb - e06265d204f6 - 2dccb6bb0add + - 782bdcb775fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - - f0216498a666 - b05f662f9f35 - 63c8377c58b3 + - f0216498a666 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: + - 8a11d70b6cd8 - c72fa6cb8817 - fe3aa71590d5 - - 8a11d70b6cd8 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccomparematrices @@ -300,49 +300,49 @@ tools: - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - a83732c79949 - 2ba6cee8e4db - c0737631eea1 + - a83732c79949 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - ea19190ce5e0 - 62b720dceb56 - 30d7390bc918 + - ea19190ce5e0 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - 2786a931cad2 - - cd40ca76865a - 2b4d6a8dab36 + - cd40ca76865a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdetectloops owner: bgruening revisions: - ffc33339cd3e - - bf9379529c3e - 0410b6aada45 + - bf9379529c3e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: - - 07dd436ea686 - 77d8e0fd162a + - 07dd436ea686 - 5dfba24d7bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: - - 972dcccb5bbc - - f1b3902f8baf - 6c5097f6d41e + - f1b3902f8baf + - 972dcccb5bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops @@ -356,48 +356,48 @@ tools: - name: hicexplorer_hicinfo owner: bgruening revisions: - - e4f8fceab96a - 51e40e9b6c3c - b0f33533181d + - e4f8fceab96a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: - - c261b6b05ee3 - 55b013e59018 + - c261b6b05ee3 - 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: + - b376ef118807 - 4b194e675916 - b6b8c8672756 - - b376ef118807 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - - ed900cd4a0a9 - - 1511a8ebe906 - 910c6a1c3a27 + - 1511a8ebe906 + - ed900cd4a0a9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - - 2aa5b6b65197 - - 6d042c96aceb - f34ab9882252 + - 6d042c96aceb + - 2aa5b6b65197 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions owner: bgruening revisions: - - dd9988943f53 - 9b383d429659 + - dd9988943f53 - ea5d67ec94ab tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -412,9 +412,9 @@ tools: - name: hicexplorer_hicplotsvl owner: bgruening revisions: + - beb5b5917d2f - 337705015ee8 - b4e780e93c91 - - beb5b5917d2f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotviewpoint @@ -428,17 +428,17 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - ea8fb5e899e8 + - 21d859ad4502 - 5cbd7a902a8d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: - - 36dfa2825a59 - - 1d6af10874d5 - f81750434d70 + - 1d6af10874d5 + - 36dfa2825a59 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -464,20 +464,20 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - cef9fb4ece1c - - 1d201e8378b3 - 11a3385e03b5 + - 1d201e8378b3 + - cef9fb4ece1c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: - - db575b4c8b22 - - 7784821452ac + - 4b0adaa31c95 - 59be31ac9dc3 - - eeab712b0b99 + - 7784821452ac + - db575b4c8b22 - e98619de2776 - - 4b0adaa31c95 + - eeab712b0b99 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -489,23 +489,23 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - - 7ffaa0968da3 - 48f0fb3061b1 + - 7ffaa0968da3 + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 8cd2ecfa2e61 - 56371b5a2da9 + - 8cd2ecfa2e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset owner: bgruening revisions: - - fde4c972e7c5 - 8c64a2da3869 + - fde4c972e7c5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_manipulate_eset @@ -523,11 +523,11 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 7e014059a88d - - f911a64454fb - - c4f39bf4a068 - a4b734cd253b + - c4f39bf4a068 + - 7e014059a88d - 49776718ae90 + - f911a64454fb tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_clustering @@ -539,10 +539,10 @@ tools: - name: raceid_filtnormconf owner: iuc revisions: + - 43c146e25a43 + - d45f092caf24 - 7608d5faee41 - 8b917923f7d4 - - d45f092caf24 - - 43c146e25a43 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf @@ -554,9 +554,9 @@ tools: - name: raceid_inspectclusters owner: iuc revisions: + - 37a47c4fd84d - 2b0d3e2f402a - c7ddb719554d - - 37a47c4fd84d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -568,8 +568,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - 69018f285aa3 + - df8e4e54d367 - 6e90c8adf84f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -582,11 +582,11 @@ tools: - name: raceid_trajectory owner: iuc revisions: - - 44b935f2271b + - e93b008c637a + - 2bfd55b87af3 - c92d0f9338c5 + - 44b935f2271b - 72979cac22b2 - - 2bfd55b87af3 - - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_trajectory @@ -610,17 +610,17 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: - - 8983e7a04ba7 - - 4d8f983cd751 - - aaa5da8e73a9 - 6acb08931836 - - 77b91b9bdf52 - - 38db3fef7aad - - b2df381a6004 + - aaa5da8e73a9 - edec35114f72 - - 6f83f8fd381f - - f9353ee6a0d4 - cb43c5d3acd3 + - b2df381a6004 + - 38db3fef7aad + - f9353ee6a0d4 + - 77b91b9bdf52 + - 8983e7a04ba7 + - 4d8f983cd751 + - 6f83f8fd381f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_cluster_reduce_dimension @@ -632,16 +632,16 @@ tools: - name: scanpy_filter owner: iuc revisions: - - a97abb8cd15b - - 64388be6d510 - - 277313130da5 - - b409c2486353 - - a03ff8633507 - 8cb783c81905 + - fc0321c000a3 - 72a6bebab2a5 + - b409c2486353 - d636ce5cde16 - - fc0321c000a3 + - a03ff8633507 + - a97abb8cd15b - 3c86f71498bc + - 277313130da5 + - 64388be6d510 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter @@ -653,17 +653,17 @@ tools: - name: scanpy_inspect owner: iuc revisions: - - 5e9171dc8244 - - c5d3684f7c4c - - f54f0f0598ad - - 18262103fa61 - d86cb2ce311b + - f54f0f0598ad - 6bd82ed14acd - - cc0deb593fc8 - 3081ff5c84a3 + - c5d3684f7c4c - 6c145a6868cc - - 5c3ebe2adc77 + - 5e9171dc8244 + - cc0deb593fc8 - c0a80a16560f + - 18262103fa61 + - 5c3ebe2adc77 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect @@ -675,17 +675,17 @@ tools: - name: scanpy_normalize owner: iuc revisions: - - 9f354c7c8c92 + - 4bda4412b8c2 + - c9cb76cf8d6c - 94c19fb1281c - d844935c906c - - 7b9fafe32c86 - - c9cb76cf8d6c - 3bcd5445cd7a + - 7b9fafe32c86 - 56c0d4acef02 - - ab55fe8030b6 - a407e7f8bdc1 - - 4bda4412b8c2 - 146ae5d70b47 + - ab55fe8030b6 + - 9f354c7c8c92 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize @@ -697,18 +697,18 @@ tools: - name: scanpy_plot owner: iuc revisions: + - aa0c474463c2 + - 6adf98e782f3 + - 62acdd96d4a0 + - 9b0cdb8cf6be - 0185bd174ea0 - 40812a65a78b - f7446fd8d5e7 - - 6adf98e782f3 - - 9b0cdb8cf6be - - 6f5349dd5c49 - 7647e5cd1b8b - - 62acdd96d4a0 + - 1072ce66b426 - dbbe1ea8ecb1 - - aa0c474463c2 + - 6f5349dd5c49 - 95777145cb92 - - 1072ce66b426 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot @@ -720,17 +720,17 @@ tools: - name: scanpy_remove_confounders owner: iuc revisions: - - fe8f16c594ec - - a39040ae0a38 - - 9fb627495ec2 - - f2f6c703da06 - - 73ab2ac53d06 - d18e7a6e5cd4 + - 73ab2ac53d06 + - f2f6c703da06 - c65fce500915 + - bf2017df9837 - 458e8f43a775 - 215733a383f2 + - a39040ae0a38 + - fe8f16c594ec + - 9fb627495ec2 - c5541bfb8feb - - bf2017df9837 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders @@ -742,9 +742,9 @@ tools: - name: scater_create_qcmetric_ready_sce owner: iuc revisions: + - 8f333f90d8d6 - b834074a9aff - fd808de478b1 - - 8f333f90d8d6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce @@ -777,8 +777,8 @@ tools: owner: iuc revisions: - 2e41b35b5bdd - - ef4c80837bc5 - 81e5bdff4853 + - ef4c80837bc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_dist_scatter @@ -796,8 +796,8 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - c99ba278dfa9 - 46fc6751d746 + - c99ba278dfa9 - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -1047,15 +1047,15 @@ tools: - name: snapatac2_peaks_and_motif owner: iuc revisions: - - 64fa083411f1 - 588c811fdd48 + - 64fa083411f1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_plotting owner: iuc revisions: - - fecf9664c885 - 05bd4db20227 + - fecf9664c885 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing @@ -1074,8 +1074,8 @@ tools: - name: velocyto_cli owner: iuc revisions: - - 90e95e9ee190 - 883c33ef3372 + - 90e95e9ee190 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: vitessce_spatial diff --git a/staging.gvl.org.au/statistics.yml b/staging.gvl.org.au/statistics.yml index 22868a413..bd5dfc98c 100644 --- a/staging.gvl.org.au/statistics.yml +++ b/staging.gvl.org.au/statistics.yml @@ -32,18 +32,18 @@ tools: - name: datamash_ops owner: iuc revisions: - - 2f3c6f2dcf39 + - 562f3c677828 - 4c07ddedc198 - 419027d822d6 - - 562f3c677828 + - 2f3c6f2dcf39 - 746e8e4bf929 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_ava_perclass owner: devteam revisions: - - b87bbe6bc044 - a0defff5cf89 + - b87bbe6bc044 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -120,43 +120,43 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - 7442b94d6a1e + - aef56d0e7a61 - 4c4ec859c31a - 9c3e1d3235c8 - - 840f29aad145 - - aef56d0e7a61 - b1eda492f063 + - 840f29aad145 + - 7442b94d6a1e tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 9fda0b82f419 + - 30d21a6041f6 - d0352e8b4c10 - 375bbd555f4a - - 30d21a6041f6 + - 9fda0b82f419 - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: - - 7ae443e6217d - - 8b1b2b91f8d0 - 4cc980df6265 - - cd02bf168d23 - 2c58b83c9bad + - 8b1b2b91f8d0 + - 7ae443e6217d + - cd02bf168d23 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - - ad7e0b4291ee + - e10e776f2109 - bb9fc9d46ea4 - - 4bbaf77573ef - 1dd433d2c92c + - 4bbaf77573ef + - ad7e0b4291ee - 7dd3fb35904f - - e10e776f2109 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: t_test_two_samples diff --git a/staging.gvl.org.au/text_manipulation.yml b/staging.gvl.org.au/text_manipulation.yml index 0c66317e2..9fcbace78 100644 --- a/staging.gvl.org.au/text_manipulation.yml +++ b/staging.gvl.org.au/text_manipulation.yml @@ -14,8 +14,8 @@ tools: - name: add_value owner: devteam revisions: - - 023f0a3760b3 - 745871c0b055 + - 023f0a3760b3 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_element_identifiers @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: + - 9cd341095afd + - 02026300aa45 - 6595517c2dd8 + - 626658afe4cb - aff5135563c6 - - 464b9305180e - 6e8d94597139 - - 9cd341095afd + - 464b9305180e - 13b6f0007d9e - - 02026300aa45 - - 626658afe4cb - be25c075ed54 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -80,10 +80,10 @@ tools: owner: iuc revisions: - 37cde8134c6a - - 90f657745fea - 557ec8d7087d - - 9cc411a62277 + - 90f657745fea - 34d29339abab + - 9cc411a62277 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: gff3_rebase @@ -108,28 +108,28 @@ tools: owner: devteam revisions: - ae7843d06f8f - - f2aac0c5c60d - dd40b1e9eebe + - f2aac0c5c60d tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: query_tabular owner: iuc revisions: - - 3a6b78c39dca - - 2e8f945f7285 - - 1ea4e668bf73 + - 83069b38aa85 - 623f3eb7aa48 - cf4397560712 + - 2e8f945f7285 + - 1ea4e668bf73 + - 3a6b78c39dca - 33d61c89fb8d - cf34c344508d - - 83069b38aa85 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: regex_find_replace owner: galaxyp revisions: - - 399da6b5ec21 - ae8c4b2488e7 + - 399da6b5ec21 - 503bcd6ebe4b tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu @@ -142,10 +142,10 @@ tools: - name: sqlite_to_tabular owner: iuc revisions: - - c4d18aa4ec4a - - bce29ec10b78 - b722161a845a + - c4d18aa4ec4a - f768f6183386 + - bce29ec10b78 tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: table_compute @@ -158,15 +158,15 @@ tools: - name: text_processing owner: bgruening revisions: - - 86755160afbf - - ddf54b12c295 - - 74a8bef53a00 - - 9ff72e942410 - - d698c222f354 - fbf99087e067 - f46f0e4f75c4 + - 74a8bef53a00 + - 0a8c6b61f0f4 + - 9ff72e942410 - a6f147a050a2 - 12615d397df7 - - 0a8c6b61f0f4 + - ddf54b12c295 + - d698c222f354 + - 86755160afbf tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/staging.gvl.org.au/variant_calling.yml b/staging.gvl.org.au/variant_calling.yml index d5e410e0c..63d2d7182 100644 --- a/staging.gvl.org.au/variant_calling.yml +++ b/staging.gvl.org.au/variant_calling.yml @@ -29,56 +29,56 @@ tools: owner: iuc revisions: - 23d7e75d850e - - cb441f258c37 - c0f8fe52948e + - cb441f258c37 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: freebayes owner: devteam revisions: - - 156b60c1530f - - 04fa42777df9 - 57def2d7c093 + - a5937157062f - ef2c525bd8cd + - 156b60c1530f + - 04fa42777df9 - 3e954e7125bf - - a5937157062f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_alnqual owner: iuc revisions: - - 791f73caa0c8 - 09d6e4693887 - - 435b157bed6d - e61c9ac190ad + - 791f73caa0c8 + - 435b157bed6d tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_call owner: iuc revisions: - 65432c3abf6c - - b11e8e9c23bf - - dfadc322b065 - 4805fe3d8fda + - 03627f24605f + - b11e8e9c23bf - 3b4b2121842f - 074d44697036 + - dfadc322b065 - e1461b5c52a0 - - 03627f24605f tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_filter owner: iuc revisions: - 701d134358ad - - 9cb929f21cfa - 7dfca164d2e3 + - 9cb929f21cfa tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: lofreq_indelqual owner: iuc revisions: - - f4473557ffc7 - c27549b9aa1f + - f4473557ffc7 - 971e07ca4456 - 426d707dfc47 tool_panel_section_label: Variant Calling @@ -86,9 +86,9 @@ tools: - name: lofreq_viterbi owner: iuc revisions: - - cdaab621d454 - - aa35ee7f3ab2 - dbd9f2db9ed8 + - aa35ee7f3ab2 + - cdaab621d454 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: naive_variant_caller @@ -100,19 +100,19 @@ tools: - name: sniffles owner: iuc revisions: + - ceff2f6a5368 - 93c4b04a0769 - 43fffeed243f - - ceff2f6a5368 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snippy owner: iuc revisions: - 5bbf9eada9c2 + - 9bccc8404a3c - c9a8ef2aa380 - - fa016f1eea1a - d220115f882b - - 9bccc8404a3c + - fa016f1eea1a tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: snp_dists @@ -155,20 +155,20 @@ tools: owner: iuc revisions: - 32f14a2723ec - - 40f0591deda0 - ee4a90760848 - e7aff4a85df5 - 3b1e7c170b10 + - 40f0591deda0 tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: tbvcfreport owner: iuc revisions: - - 42818629ec4c + - 9793bc5d741b - adc0645b945c + - 42818629ec4c - 02d81b994ef5 - 4934c0ac6197 - - 9793bc5d741b tool_panel_section_label: Variant Calling tool_shed_url: toolshed.g2.bx.psu.edu - name: varscan_copynumber diff --git a/staging.gvl.org.au/vcfbcf.yml b/staging.gvl.org.au/vcfbcf.yml index 826250d9b..34fcb9424 100644 --- a/staging.gvl.org.au/vcfbcf.yml +++ b/staging.gvl.org.au/vcfbcf.yml @@ -2,14 +2,14 @@ tools: - name: bcftools_annotate owner: iuc revisions: - - 265fe0f9ea64 - - 6a88248893c4 - 2c372041ed8c - ebe5fc018e72 + - e075b1be5abb + - 95815a0bb307 + - 265fe0f9ea64 - b7ea370b8f5d + - 6a88248893c4 - 8a2e296c07ef - - 95815a0bb307 - - e075b1be5abb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_annotate @@ -21,13 +21,13 @@ tools: - name: bcftools_call owner: iuc revisions: - - b03984136ce4 - 22637b1a55bf - - 0fba2c15b40d - - 1001172b5089 + - 544cb432072b + - b03984136ce4 - 21687e35f066 - c37b684e7f4e - - 544cb432072b + - 1001172b5089 + - 0fba2c15b40d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_call @@ -39,15 +39,15 @@ tools: - name: bcftools_cnv owner: iuc revisions: - - bf1f4994f104 - - 01d6b7d6365e + - 8627b2b383b4 + - 8ca3647c90fd - 0238f68ad641 - - ccb83bf54de0 + - 01d6b7d6365e - 143796b504eb + - ccb83bf54de0 - 3a7084316a6e - - 8ca3647c90fd - - 8627b2b383b4 - 8408bffd5616 + - bf1f4994f104 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_cnv @@ -59,13 +59,13 @@ tools: - name: bcftools_concat owner: iuc revisions: - - d144af39073a - 62ca6da715bf - - 6b6c992d3a14 - f430a1ec7ee4 - 03e0645395d2 - 9b5abbf50d23 + - d144af39073a - abd489215f73 + - 6b6c992d3a14 - 81426b3cf18b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -79,13 +79,13 @@ tools: owner: iuc revisions: - 2363ef414c9b - - d37e313a41be + - 95c6f3f4c77f + - 1829900b5dcd - 1171446da5db - d3081540d175 - - e522022137f6 - 8aa352093d73 - - 1829900b5dcd - - 95c6f3f4c77f + - d37e313a41be + - e522022137f6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_consensus @@ -97,14 +97,14 @@ tools: - name: bcftools_convert_from_vcf owner: iuc revisions: + - b14ff40958cb - 348cd212dbad - 09f37afb3621 - - 1137ce8efc1e - - d58d2e8c7a57 - 012656fd329f - 92c0aff8b53e - 9b29129fb491 - - b14ff40958cb + - d58d2e8c7a57 + - 1137ce8efc1e tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_from_vcf @@ -116,13 +116,13 @@ tools: - name: bcftools_convert_to_vcf owner: iuc revisions: - - 367ba501b6eb - - 1f2183a23823 - - ecc9192912b8 - 55c0e906c14c - 7291189e98b4 + - 1f2183a23823 - de68c11034f6 + - ecc9192912b8 - cfd81f17580b + - 367ba501b6eb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_convert_to_vcf @@ -134,13 +134,13 @@ tools: - name: bcftools_csq owner: iuc revisions: + - e6f4badbe6f3 - ae68ceb4cca3 + - 6c790a091c7c + - d237eaef451f - 7cbf3c66d4ad - 039ea3f1dea9 - - d237eaef451f - - e6f4badbe6f3 - 64a8f7dae3ad - - 6c790a091c7c tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_csq @@ -152,14 +152,14 @@ tools: - name: bcftools_filter owner: iuc revisions: - - 46fcafba49ec - 5d6653c989cb + - 963a3635b2e1 - 33bd9301568c - - e7452697afd9 + - 46fcafba49ec - 6ea7170a016d - - 963a3635b2e1 - 277719af4dd7 - cdb7b4927742 + - e7452697afd9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_filter @@ -172,13 +172,13 @@ tools: owner: iuc revisions: - a1213a0b7b66 + - 5a321fab1fe4 + - 26d97cdd5410 - 501bfb078342 - a29a2f40b665 - - 5a321fab1fe4 + - 7b4454382d39 - 91c1e57d5c7f - b7f0f59baa7e - - 7b4454382d39 - - 26d97cdd5410 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_gtcheck @@ -190,15 +190,15 @@ tools: - name: bcftools_isec owner: iuc revisions: - - c803c34361e0 - - 15da1ddcfeff - - 768d04526638 - - 5f27e814a119 - - d7d1663559e9 - - 81e4014fa809 - 97d19c008d15 - 709dd8291b83 + - 768d04526638 + - 15da1ddcfeff - 39bca000353d + - 81e4014fa809 + - 5f27e814a119 + - d7d1663559e9 + - c803c34361e0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_isec @@ -211,13 +211,13 @@ tools: owner: iuc revisions: - 5b006286a458 - - 86296490704e + - b931e65638b8 - 7ba36babba2d - - b84fda8ebef0 - 2215287d5cc9 - - 85ee7e6c4204 + - 86296490704e - b1eba148b35b - - b931e65638b8 + - 85ee7e6c4204 + - b84fda8ebef0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_merge @@ -229,16 +229,16 @@ tools: - name: bcftools_mpileup owner: iuc revisions: - - f506df85c652 - - 5660b21a0dbd - - 56556e1267de - - 9c711df3258d - ce9396ddcb2b + - f506df85c652 - 0a5dcc9a8ec2 + - cf06b44624c7 - 4e1d23e5c691 + - 5660b21a0dbd + - 9c711df3258d + - 56556e1267de - 31ea13dfe5e6 - 37757ffb4c5f - - cf06b44624c7 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_mpileup @@ -251,12 +251,12 @@ tools: owner: iuc revisions: - 1ca7418e46ee - - a404f786a94c - - 19905c025d2a - - 48291658fdf6 - 271965b55437 - 6deb4d549bc9 + - 48291658fdf6 - 021693fdadaa + - a404f786a94c + - 19905c025d2a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_norm @@ -268,14 +268,14 @@ tools: - name: bcftools_plugin_counts owner: iuc revisions: - - dadbd61dc4cf + - f7879f1e77f9 + - 69d8b7567281 + - 3f6fadf8b8ff + - 5ad5d4243987 - 97e8145d7e30 - c450406f722b - - 3f6fadf8b8ff - - 69d8b7567281 - - f7879f1e77f9 - 71c78e0eea52 - - 5ad5d4243987 + - dadbd61dc4cf tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_counts @@ -287,14 +287,14 @@ tools: - name: bcftools_plugin_dosage owner: iuc revisions: - - 79f7a1acc2cd - - 2514e684f8a3 - - 283911fe7e1a - - 0fe007201caf - d31a2e310a52 + - 52f9e4a660e3 + - 79f7a1acc2cd - cc7f9a4e186b - 6cf13a657cf6 - - 52f9e4a660e3 + - 0fe007201caf + - 283911fe7e1a + - 2514e684f8a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_dosage @@ -306,14 +306,14 @@ tools: - name: bcftools_plugin_fill_an_ac owner: iuc revisions: - - 75ddd081f608 - - 80e6e399ccd0 - - a12844ca467a + - 0a62420cb9cd - 026a989b7cee - - 230e424bde67 - - 6963a6841d22 + - a12844ca467a + - 75ddd081f608 - 1411bef27a75 - - 0a62420cb9cd + - 6963a6841d22 + - 230e424bde67 + - 80e6e399ccd0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_an_ac @@ -325,14 +325,14 @@ tools: - name: bcftools_plugin_fill_tags owner: iuc revisions: - - b10d1510fa84 - - 5acfca5a76af - - bca7ce81688f - - 5808f77b2bb6 - - e493702b19eb - - 450a265f92e8 - 444e6a756c35 - ba20340426fe + - bca7ce81688f + - 450a265f92e8 + - 5acfca5a76af + - e493702b19eb + - 5808f77b2bb6 + - b10d1510fa84 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fill_tags @@ -344,14 +344,14 @@ tools: - name: bcftools_plugin_fixploidy owner: iuc revisions: - - dd72ff87cfd0 - - 68fec03a63b7 - - c43399f161f4 - - f2482aa4862e - - 157ffcdd3fa7 - 12152af85697 - 4d236c696844 - d52b8947b269 + - 68fec03a63b7 + - 157ffcdd3fa7 + - c43399f161f4 + - f2482aa4862e + - dd72ff87cfd0 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_fixploidy @@ -363,13 +363,13 @@ tools: - name: bcftools_plugin_impute_info owner: iuc revisions: - - cbe39e530cbf - - 29ba253e2e05 - 8f2fc0ab30fb - - 75becf493cd3 + - 29ba253e2e05 - 8dbce095986c + - cbe39e530cbf - 0e5d11004815 - 6f8e223f78f3 + - 75becf493cd3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_impute_info @@ -381,13 +381,13 @@ tools: - name: bcftools_plugin_mendelian owner: iuc revisions: + - a367a15c6de5 + - 3ff5654b4e7d - a8630d4fbaf8 - 88bb477f45f7 - - 8f5962c43868 - - a367a15c6de5 - - e0a856def0b0 - 9708e3086f32 - - 3ff5654b4e7d + - e0a856def0b0 + - 8f5962c43868 - f544f71adb73 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -400,14 +400,14 @@ tools: - name: bcftools_plugin_missing2ref owner: iuc revisions: - - 03e30f06f15f + - 4ed46189d6c6 + - 34dc0bbc7e93 - 8b260d252ff4 - - 5c9729d54721 - 31c096c6b156 - - 4ed46189d6c6 - - 96d0145c041a + - 03e30f06f15f - 6ce175385dd9 - - 34dc0bbc7e93 + - 5c9729d54721 + - 96d0145c041a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_missing2ref @@ -419,14 +419,14 @@ tools: - name: bcftools_plugin_setgt owner: iuc revisions: - - 46eb13bc2c73 + - a730269af659 + - 681bdf1e22ff - 40daf124be88 - - a1aad8b559c6 + - 09f5e45a8212 - 2c4941386820 - - 681bdf1e22ff + - 46eb13bc2c73 + - a1aad8b559c6 - 11af7fce71cf - - 09f5e45a8212 - - a730269af659 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_setgt @@ -438,15 +438,15 @@ tools: - name: bcftools_plugin_tag2tag owner: iuc revisions: - - f272b8ba0983 - - b74b8cbfc1f1 - - 8cb121b6a1d2 - 0594ea1417c8 + - 6cbb9c47795c + - b74b8cbfc1f1 + - f272b8ba0983 - 12038f59c0f4 + - 743cd1472aeb + - 8cb121b6a1d2 - 3897eaadfbff - - 6cbb9c47795c - 882b2e649602 - - 743cd1472aeb tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_plugin_tag2tag @@ -458,13 +458,13 @@ tools: - name: bcftools_query_list_samples owner: iuc revisions: - - a9826db86d9a - - 238f78e38a8b - - cced6715f926 - - eccb508bb678 - - adee7e8b746f - 18cf9de1cf73 + - adee7e8b746f - dba06328556a + - a9826db86d9a + - eccb508bb678 + - cced6715f926 + - 238f78e38a8b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query_list_samples @@ -476,14 +476,14 @@ tools: - name: bcftools_query owner: iuc revisions: - - e53501abf992 - f64e7ca2efd2 - - c9935c9e8a24 - - 9f36041495a3 - - 3ce32adc55b2 + - fdec14f69010 - e0ad88dec40d - 31a1b89eab9b - - fdec14f69010 + - c9935c9e8a24 + - 3ce32adc55b2 + - e53501abf992 + - 9f36041495a3 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_query @@ -495,14 +495,14 @@ tools: - name: bcftools_reheader owner: iuc revisions: + - d68c43202172 - 4db0695a6fc7 + - 2331ddcbd5aa - 3b7b1fe7b937 - - b7be725976b6 + - fd3539749127 - 79489d5685dd - - 2331ddcbd5aa - d43eb39b989e - - d68c43202172 - - fd3539749127 + - b7be725976b6 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_reheader @@ -514,13 +514,13 @@ tools: - name: bcftools_roh owner: iuc revisions: - - b0d39ef600a7 - - 5296d26b0373 - - 1a989b4110da - - 6a636d58dfc2 - 1ccf0e7fb4f6 + - 6a636d58dfc2 - 78cd8b69da4c - 58091e1be01b + - b0d39ef600a7 + - 5296d26b0373 + - 1a989b4110da tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_roh @@ -532,13 +532,13 @@ tools: - name: bcftools_stats owner: iuc revisions: - - baa8823f8073 - 591cc8518033 - bf8325a07ce7 - - b641062a2587 - e8af591435d1 + - baa8823f8073 - '388983871932' - 4d3ce9dc1525 + - b641062a2587 - b17394940c7a tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu @@ -552,13 +552,13 @@ tools: owner: iuc revisions: - c2ab91a0d506 + - d1f8f55f564d + - 38d75661c235 - 1a2ef636f48e - 59fa8742285e - - 3ca3de4e5291 - e6b5cbbf449b - - d1f8f55f564d - - 38d75661c235 - 3a233c8eb814 + - 3ca3de4e5291 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: bcftools_view @@ -570,8 +570,8 @@ tools: - name: vcf2tsv owner: devteam revisions: - - 285060661b45 - e92b3c0f9224 + - 285060661b45 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfaddinfo @@ -591,8 +591,8 @@ tools: - name: vcfannotate owner: devteam revisions: - - 01e0321aca98 - 6faa2c4c71d2 + - 01e0321aca98 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfannotategenotypes @@ -619,8 +619,8 @@ tools: - name: vcfcheck owner: devteam revisions: - - 5e850c85ba32 - aa8e8c96ca06 + - 5e850c85ba32 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfcombine @@ -648,15 +648,15 @@ tools: owner: devteam revisions: - 4bdc111b2470 - - 6b935ab36d7b - eae7c08ebb6f + - 6b935ab36d7b tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcffixup owner: devteam revisions: - - fc5a64fdd5b2 - 11f62f071125 + - fc5a64fdd5b2 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfflatten @@ -669,8 +669,8 @@ tools: - name: vcfgeno2haplo owner: devteam revisions: - - a3dea556218d - b890055e07bd + - a3dea556218d tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfgenotypes @@ -690,8 +690,8 @@ tools: - name: vcfleftalign owner: devteam revisions: - - d2406f98a782 - 29f9b782727e + - d2406f98a782 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfprimers @@ -711,15 +711,15 @@ tools: - name: vcfselectsamples owner: devteam revisions: - - 2ba3b87f904f - 958b6484a7f1 + - 2ba3b87f904f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcfsort owner: devteam revisions: - - ee60203e68d9 - 5b7120c66efc + - ee60203e68d9 tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu - name: vcftools_annotate @@ -749,7 +749,7 @@ tools: - name: vcfvcfintersect owner: devteam revisions: - - 166c4f50525f - 6f6bf10618d7 + - 166c4f50525f tool_panel_section_label: VCF/BCF tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/annotation.yml b/usegalaxy.org.au/annotation.yml index fba91387c..35d3c8d7a 100644 --- a/usegalaxy.org.au/annotation.yml +++ b/usegalaxy.org.au/annotation.yml @@ -2,18 +2,18 @@ tools: - name: abricate owner: iuc revisions: - - 3f3e247c053d - - 78c75f134c16 + - 4efdca267d51 - c2ef298da409 - 6e9aea89e388 - - 4efdca267d51 + - 3f3e247c053d + - 78c75f134c16 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_canongff3 owner: iuc revisions: - - c45c9dd066e2 - 3f438bf5475d + - c45c9dd066e2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_gaeval @@ -26,30 +26,30 @@ tools: - name: aegean_locuspocus owner: iuc revisions: - - c4ac24510b55 - 1fdc517743e6 + - c4ac24510b55 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: aegean_parseval owner: iuc revisions: - - 1b52f0c8ad7f - d6c074a93c51 + - 1b52f0c8ad7f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: annotatemyids owner: iuc revisions: - - fe3ca740a485 + - 3e1f6f6d557e + - a79ee60b6926 - 133f36c29579 - - 4f2967b27e67 - 44018dd6b447 - - 3e1f6f6d557e - - cd2480f35935 - - 1aae04680c4b - f29602ae449e - - a79ee60b6926 + - fe3ca740a485 - b5d8e5475247 + - cd2480f35935 + - 4f2967b27e67 + - 1aae04680c4b tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: antismash @@ -62,10 +62,10 @@ tools: - name: augustus_training owner: bgruening revisions: - - f1e653756174 - - dc027fa56d55 - 7be22100e5e1 + - dc027fa56d55 - 6519ebe25019 + - f1e653756174 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: augustus @@ -73,17 +73,17 @@ tools: revisions: - 09855551d713 - ca6d970d931c - - bd0e53f3a891 - 28433faa6e42 + - bd0e53f3a891 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: bakta owner: iuc revisions: - - da5f1924bb2e - d77802fe76f7 - - 728dacaf08a9 - 92eee5f31117 + - da5f1924bb2e + - 728dacaf08a9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: barrnap @@ -103,8 +103,8 @@ tools: - name: chipseeker owner: rnateam revisions: - - 8bd92f2404dd - 1b9a9409831d + - 8bd92f2404dd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: compleasm @@ -116,17 +116,17 @@ tools: - name: cpat owner: bgruening revisions: - - 8e9e228c54c4 - 7ccc6234b54e - 1ac12c0cc7a0 + - 8e9e228c54c4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: eggnog_mapper owner: galaxyp revisions: - - d9c3016f7283 - - 63662ae295d6 - 9d1fbff733cf + - 63662ae295d6 + - d9c3016f7283 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: exonerate @@ -157,60 +157,60 @@ tools: owner: iuc revisions: - 3bbe70fef6df + - 756376aeb1ae - 9f2455341fac - - b6b5cd37f2a2 - - 9c15ca7e764e - 14f588312c56 - 582fd74dc2a1 - - 756376aeb1ae + - 9c15ca7e764e + - b6b5cd37f2a2 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_clean owner: iuc revisions: - - a230ea445788 - - 73428a792541 + - 989f7c061f35 - 8e1ace8f77c6 - 0ffe5be70caf - - 1691af4a0d17 - 30fb23d4c31c - - 989f7c061f35 + - a230ea445788 + - 1691af4a0d17 + - 73428a792541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_compare owner: iuc revisions: - 5a5ae61da69c - - 494f0bb4a993 - 0418d28136de - - 563a19373357 - - 30f08d74024f - 57c6718cbfcc + - 563a19373357 - e94187d661df + - 494f0bb4a993 + - 30f08d74024f tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_predict owner: iuc revisions: - - f77d7b685bb3 - - 2bba2ff070d9 - - 1bc5a03faf2e - 4b96ced19f75 + - f77d7b685bb3 - d6c7106b7b2e - 7abc5f6dd595 - f31125bb85ea + - 1bc5a03faf2e + - 2bba2ff070d9 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: funannotate_sort owner: iuc revisions: - - d3af38b9c7e1 + - d77fdcca400e - b3cf4684e9c7 - 520e30695ec3 - - d77fdcca400e - fed64e676186 - - 54961e026fe4 + - d3af38b9c7e1 - 52af33194019 + - 54961e026fe4 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: get_orfs_or_cdss @@ -223,8 +223,8 @@ tools: owner: iuc revisions: - 2aea122fbd25 - - 79261884facd - 07d7991bf205 + - 79261884facd tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goenrichment @@ -236,10 +236,10 @@ tools: - name: goseq owner: iuc revisions: + - 43798b4caee0 - 602de62d995b - 8b3e3657034e - ef2ad746b589 - - 43798b4caee0 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: goslimmer @@ -263,16 +263,16 @@ tools: - name: infernal owner: bgruening revisions: - - c9e29ac5d099 - 477d829d3250 + - c9e29ac5d099 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: interproscan owner: bgruening revisions: - - 98cafcbd2578 - 74810db257cc - c55643c3d813 + - 98cafcbd2578 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: jcvi_gff_stats @@ -290,24 +290,24 @@ tools: - name: maker_map_ids owner: iuc revisions: - - 326f9c294b09 - e906fa778440 + - 326f9c294b09 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: maker owner: iuc revisions: - d46d803ca6cc - - 370c210d9541 - 3c1a01127868 + - 370c210d9541 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: mitos2 owner: iuc revisions: + - c8ac28e8ac44 - e95d52d295d7 - 624606f7c996 - - c8ac28e8ac44 - b815ec682418 - 033755194fe9 tool_panel_section_label: Annotation @@ -357,9 +357,9 @@ tools: - name: prokka owner: crs4 revisions: - - bf68eb663bc3 - - d643e3b03500 - 8a22554cdde2 + - d643e3b03500 + - bf68eb663bc3 - a17498c603ec tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu @@ -379,8 +379,8 @@ tools: - name: repeatmodeler owner: csbl revisions: - - 8661b2607b7e - 41bfbaf3c959 + - 8661b2607b7e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sanntis_marine @@ -404,30 +404,30 @@ tools: - name: snpeff owner: iuc revisions: + - c7275bd8b4d6 - 68693743661e - - 5c7b70713fb5 - - 5b80f544c67f - - 5a29ab10dba6 + - 268d162b9c49 - cfcf33df7fc0 - - 6322be79bd8e + - 5a29ab10dba6 + - 5b80f544c67f + - 5c7b70713fb5 - 8f92c2b26e6d - - c7275bd8b4d6 - - 268d162b9c49 + - 6322be79bd8e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: snpsift owner: iuc revisions: - - 09d6806c609e - 5fab4f81391d - 2b3e65a4252f + - 09d6806c609e tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: sortmerna owner: rnateam revisions: - - eb35257d2e29 - 10b84b577117 + - eb35257d2e29 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: tbl2gff3 @@ -439,25 +439,25 @@ tools: - name: tbprofiler owner: iuc revisions: - - 809dfc93d593 - - 037a11682176 - - ac8250086ac3 - 51dd22484644 - - e1a9d6fd258d - - d03af1c7002c - - 45083d070fb8 - - 200c378d85f3 + - ba6f87115e13 - 4839e590cb26 + - ac8250086ac3 + - 200c378d85f3 - 8cb134b8c1a5 - 37213cf56392 - - ba6f87115e13 + - 037a11682176 + - 45083d070fb8 + - e1a9d6fd258d + - d03af1c7002c + - 809dfc93d593 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_gumbel owner: iuc revisions: - - 8fc50fe60127 - f50807720df1 + - 8fc50fe60127 tool_panel_section_label: Annotation tool_shed_url: toolshed.g2.bx.psu.edu - name: transit_hmm diff --git a/usegalaxy.org.au/assembly.yml b/usegalaxy.org.au/assembly.yml index c28a2f149..030b740a0 100644 --- a/usegalaxy.org.au/assembly.yml +++ b/usegalaxy.org.au/assembly.yml @@ -3,27 +3,27 @@ tools: owner: iuc revisions: - a929ce596a34 - - 890b794c997d - - 841084c5fc46 - - 8f1b150a2487 + - fa5259cc561b - d6d5ccc2c581 - - 553bfe8bd0b5 - - 0e93176640ac - - db9b10824c61 + - 8f1b150a2487 + - 890b794c997d - 7547fcab5d19 - 0124fce4654a - - fa5259cc561b + - db9b10824c61 + - 0e93176640ac + - 553bfe8bd0b5 + - 841084c5fc46 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bandage owner: iuc revisions: - 21e491ad532a - - 94fe43e75ddc - - b9e31c5c01c7 - - b2860df42e16 - ddddce450736 - 067592b6b312 + - b9e31c5c01c7 + - b2860df42e16 + - 94fe43e75ddc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: bellerophon @@ -37,47 +37,47 @@ tools: owner: bgruening revisions: - a7f16f24e9a1 - - 22286dab5aa1 - - 3371c5bdc17a - faee8629b460 - 5258e18bbe23 + - 3371c5bdc17a + - 22286dab5aa1 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: blobtoolkit owner: bgruening revisions: - - '392811378515' - 53dd00a4ab68 + - '392811378515' tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: busco owner: iuc revisions: - - 94170eee0ad8 - - 41030a6c03b7 + - 5ecdeca79a0d - e4bd1e99bacf - - 2dd755c1c6ff - 2babe6d5c561 - - 602fb8e63aa7 + - 46ae58b1d792 + - 2dd755c1c6ff + - 94170eee0ad8 + - bb935709506a - 4048d82f0c88 - - 5ecdeca79a0d + - cf13a1e03e5b + - 41030a6c03b7 + - 602fb8e63aa7 - ea8146ee148f - 1440ae06552f - - e5c372c91e46 - - 46ae58b1d792 - - cf13a1e03e5b - e824f5d958d0 - - bb935709506a - - 1e62c28ba91d + - e5c372c91e46 - 0d243f458b53 + - 1e62c28ba91d tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: canu owner: bgruening revisions: - - 5732f959936a - c5b7390290b1 - 86f150c8019d + - 5732f959936a tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: cap3 @@ -89,42 +89,42 @@ tools: - name: flye owner: bgruening revisions: + - 3ee0ef312022 + - 291923e6f276 - 3e4f8642c77e - - cb8dfd28c16f - - 276f5d8712d5 - 1f0769f0b56b + - 8d4f03b5fe9d - e27815e82dd4 + - cb8dfd28c16f + - 276f5d8712d5 - 1ce9b1d72ec3 - - 8d4f03b5fe9d - - 3ee0ef312022 - - 291923e6f276 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: genomescope owner: iuc revisions: - - b2f674562a18 - - 01210c4e9144 - 460fad600dce - 3169a38c2656 + - b2f674562a18 + - 01210c4e9144 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: getorganelle owner: iuc revisions: + - 06bcf65179fb - 8b330a577046 - ba88bc5a6446 - - 06bcf65179fb - 7348b69e5109 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: gfastats owner: bgruening revisions: - - 690c2caa367e - f4a3eff8ab85 - - 3fba9c77550a - 6ec1b853c8fd + - 3fba9c77550a + - 690c2caa367e - 3ef480892a9f - 5127a713de83 tool_panel_section_label: Assembly @@ -138,24 +138,24 @@ tools: - name: hifiasm owner: bgruening revisions: - - 60024a528cbd - - 5161f204ba63 - - 0ee0c3089254 - - 71740308d412 - - 284a1cb82b61 + - ec9e21e9c71b + - 2061fb3b81b4 - 5bec28269d95 + - 5161f204ba63 + - df25d4fb79b7 + - 41cea2aa2dce - 3f7be05a1597 - - ec9e21e9c71b - - 9ef6920c3089 - - 045c7c3d8e59 - 366a11d316a7 - - 41cea2aa2dce - f3c89da3af16 - - 5f625c63b8bc - - da9d8bf98802 - - 2061fb3b81b4 - - df25d4fb79b7 - 6505bd37670d + - 9ef6920c3089 + - 0ee0c3089254 + - 60024a528cbd + - da9d8bf98802 + - 71740308d412 + - 045c7c3d8e59 + - 284a1cb82b61 + - 5f625c63b8bc tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: links @@ -179,43 +179,43 @@ tools: - name: megahit owner: iuc revisions: + - 14ddfc8ffb93 + - a96f3ad4e0d8 - de387b2b2803 - 7518ee87b53d - - a96f3ad4e0d8 - - 14ddfc8ffb93 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: merqury owner: iuc revisions: + - d7edbc9c3a07 + - f8113c25bc6b + - 9d79beb19ac3 - 39edec572bae - 09c589057ee8 - eb7b00ec347d - - 9d79beb19ac3 - - d7edbc9c3a07 - - f8113c25bc6b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: meryl owner: iuc revisions: - eadfd71dde37 - - 51c2360aa807 - 29dabd8db6f2 + - 51c2360aa807 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: metaspades owner: nml revisions: - - f369ef5f210b - - 606b09cc9860 - 2ecf5a570907 - - 99ecfdafc64f - - eb7a370f6588 - - e731ea24e48d - - f338e9942b27 - fd128c111ab0 + - e731ea24e48d + - eb7a370f6588 - 3ca2d2a9068c + - 99ecfdafc64f + - f338e9942b27 + - 606b09cc9860 + - f369ef5f210b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: minia @@ -227,11 +227,11 @@ tools: - name: miniasm owner: iuc revisions: - - 8b6d0d85252b - - b799a615995d - a7b889b90140 + - b799a615995d - 8dee0218ac7d - 73a3846701e1 + - 8b6d0d85252b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: mitobim @@ -249,9 +249,9 @@ tools: - name: novoplasty owner: iuc revisions: - - 15200570e926 - - 7c2f5268d01c - 64a1c751d99b + - 7c2f5268d01c + - 15200570e926 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: pilon @@ -263,46 +263,46 @@ tools: - name: pretext_map owner: iuc revisions: + - 02831bf9e95f + - c6cec5ab35c1 + - 2b16ba799da9 - 8fef980d48b5 - d256a51a656b - - dfb8a4497339 - - 2b16ba799da9 - - c6cec5ab35c1 - bbe19ef04a74 - - 02831bf9e95f + - dfb8a4497339 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: purge_dups owner: iuc revisions: + - 76d4cbefff85 - a315c25dc813 - e9bd16ba5ebd - - 76d4cbefff85 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: quast owner: iuc revisions: - - 342a1d1fed7b - 675488238c96 + - 875d0f36d66f + - 6fcbee531de6 + - 7594365c546b - 3061c8b029e5 - 72472698a2df + - 342a1d1fed7b - ebb0dcdb621a - - 7594365c546b - 59db8ea8c845 - - 875d0f36d66f - - 6fcbee531de6 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: racon owner: bgruening revisions: + - cd06929b224b - d865b62f501c - 78c533842eeb - - a199cd7ac344 - - cd06929b224b - aa39b19ca11e - 39bed8de8017 + - a199cd7ac344 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: ragtag @@ -314,19 +314,19 @@ tools: - name: raven owner: iuc revisions: - - 2b2a352488fa - - f11b994b7eb2 + - f8564b2d7f63 - 3edba9afc9bc - 33b7d8481a76 - - f8564b2d7f63 + - 2b2a352488fa - 5c55448d0f33 + - f11b994b7eb2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaquast owner: iuc revisions: - - f73ab5187eed - 8e66f695d859 + - f73ab5187eed tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: rnaspades @@ -334,11 +334,11 @@ tools: revisions: - 28189050e437 - 5fc94b3a4704 - - 378e55aeeb25 - 53c2bc8c2ae3 - e122f9101584 - - 1d06c8b38e77 - ef69617ecb42 + - 378e55aeeb25 + - 1d06c8b38e77 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: shasta @@ -350,78 +350,78 @@ tools: - name: shovill owner: iuc revisions: - - 83ead2be47b2 - - 865119fcb694 + - d9f6a00b6db7 - ee17a294d3a3 + - 83ead2be47b2 - ad80238462c1 - f698c7604b3b - - d9f6a00b6db7 - 196a599ec43d + - 865119fcb694 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: smudgeplot owner: galaxy-australia revisions: + - 015283de3004 - 24e471d13fe9 - 5e0825476fb7 - - 015283de3004 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_biosyntheticspades owner: iuc revisions: - 1bb12736175c - - 604782a8a53a - - c33a476f4001 - 1fc82fe7ebef - 051fd2db8a27 - - 904bf932cf78 - 7490b213baa9 + - 604782a8a53a + - 904bf932cf78 + - c33a476f4001 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_coronaspades owner: iuc revisions: + - d6e617c4e338 - 9678993ca5bd - 655fa188c3cc - 808b3a0a6716 - - ad8b536d1caa - - d6e617c4e338 - fee85957cebe - 34305b013402 + - ad8b536d1caa tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaplasmidspades owner: iuc revisions: + - b8002c3f7141 + - 6b5a5842531e - 8d4b90bf9caf - e5a3b75a271f - - 037f9927c4ff - 7e27faaad80e + - 037f9927c4ff - 21da31ed41a1 - - b8002c3f7141 - - 6b5a5842531e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_metaviralspades owner: iuc revisions: + - 7922870efcca + - 5b26685e5d3b + - 2a10645aeadd + - f1532cb33c75 - 9de69775f512 - - 328aa71f0f3c - 86f66ab58e14 - - f1532cb33c75 - - 2a10645aeadd - - 5b26685e5d3b - - 7922870efcca + - 328aa71f0f3c tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades_plasmidspades owner: iuc revisions: - - 340bc17f49cf + - 6aad515a5270 - e41dcb0e913b + - 340bc17f49cf - 8cc856b935ee - - 6aad515a5270 - 85fb02c43042 - 1708851f8804 tool_panel_section_label: Assembly @@ -429,110 +429,110 @@ tools: - name: spades_rnaviralspades owner: iuc revisions: + - 6357b127161e - d159735a6a9f + - d5fb354f745d + - 249f6a28c751 - de1260f8a300 - b65a43f70b99 - - 249f6a28c751 - b3490b036c5a - - d5fb354f745d - - 6357b127161e tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: spades owner: nml revisions: - - a90db5dbaaf3 - dd7ad84f3943 - - d5887ace0dd4 - - d2d1df21dfb9 + - 33368fec3b70 - 7897763d14ec - 9006e5836729 - - 33368fec3b70 - b7829778729f + - a90db5dbaaf3 + - d5887ace0dd4 + - d2d1df21dfb9 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_cluster owner: iuc revisions: - - 505a9833ab5d - - 8f631679571f - - ced385aa976d - 189e837009c9 - - 0368ac680e70 + - ced385aa976d + - 505a9833ab5d - 6f4c8ad6ea01 + - 0368ac680e70 + - 8f631679571f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_consensus owner: iuc revisions: - - a7ed21de23fe - - 9ded6109434a - - d40ed4eb0c0e - 19bdfd1e6fe3 - - 356afed970b4 + - d40ed4eb0c0e - e59bee4565b3 + - 9ded6109434a + - 356afed970b4 + - a7ed21de23fe tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_partition owner: iuc revisions: - ebd801e712bc - - 4688ae3b49b5 - - b23249f81bc4 - - 6dd935e4984b - 7673a6c920b2 + - b23249f81bc4 - 80a17897564d + - 4688ae3b49b5 + - 6dd935e4984b tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_reconcile_msa owner: iuc revisions: - - cb1e3db43020 - b5e35a2ca4f3 - - 937ea677d437 - ed312479d9eb + - cb1e3db43020 - b64696992ee9 - 59bd28f6265d + - 937ea677d437 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: trycycler_subsample owner: iuc revisions: - - 6015aa0303f2 - - b9b0246a2be3 - - 383bb5ad32e2 + - 2628f6790eda - cb4768eeca3b - 05bd7504fdb2 - - 2628f6790eda + - 383bb5ad32e2 + - b9b0246a2be3 + - 6015aa0303f2 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: unicycler owner: iuc revisions: + - 8f9f06995f98 + - 6e26c9afd301 + - e022dff952df - e92675014ac9 - - 3e44ef016b45 - 0a3a602cd1e3 - - e022dff952df - - 6e26c9afd301 - 9e3e80cc4ad4 - - 8f9f06995f98 + - 3e44ef016b45 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvet owner: devteam revisions: - - 5da9a0e2fb2d - - 920677cd220f - 8d09f8be269e + - 5da9a0e2fb2d - 08256557922f + - 920677cd220f tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: velvetoptimiser owner: simon-gladman revisions: + - 37d88f41c810 - 82398ba86ba7 - 4a53b89fa703 - - 37d88f41c810 tool_panel_section_label: Assembly tool_shed_url: toolshed.g2.bx.psu.edu - name: verkko diff --git a/usegalaxy.org.au/bacterial_typing.yml b/usegalaxy.org.au/bacterial_typing.yml index d6977d7c5..7d98e94db 100644 --- a/usegalaxy.org.au/bacterial_typing.yml +++ b/usegalaxy.org.au/bacterial_typing.yml @@ -2,19 +2,19 @@ tools: - name: integron_finder owner: iuc revisions: + - 4768f7f8e93f - bfd290fe1588 - 392f100eebcd - - 4768f7f8e93f - 1ae00120dd24 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: mlst owner: iuc revisions: - - 8e8dc9a1e3e5 - 1f5641a52664 - - ded48b36f3b7 - 31812e7a1315 + - ded48b36f3b7 + - 8e8dc9a1e3e5 tool_panel_section_label: Bacterial Typing tool_shed_url: toolshed.g2.bx.psu.edu - name: sistr_cmd diff --git a/usegalaxy.org.au/bb_tools.yml b/usegalaxy.org.au/bb_tools.yml index 7f5958101..a765a2481 100644 --- a/usegalaxy.org.au/bb_tools.yml +++ b/usegalaxy.org.au/bb_tools.yml @@ -4,25 +4,25 @@ tools: revisions: - 159b04e36791 - 0840ba83860c - - 204a131e47db + - 7beb76ffbc0f - a9c9d768b751 + - d1f62024a08b - 1c427e24fb79 - - 7beb76ffbc0f - d58c27d2c5a7 - - d1f62024a08b + - 204a131e47db tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_bbmerge owner: iuc revisions: - - 1bb2b5b52030 - cab19c0452c4 + - 1bb2b5b52030 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: bbtools_tadpole owner: iuc revisions: - - 0ddf147d1897 - ce13b4678f18 + - 0ddf147d1897 tool_panel_section_label: BB Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/bed.yml b/usegalaxy.org.au/bed.yml index b00adf5d0..52bd79064 100644 --- a/usegalaxy.org.au/bed.yml +++ b/usegalaxy.org.au/bed.yml @@ -2,17 +2,17 @@ tools: - name: bedtools owner: iuc revisions: - - 07e8b80f278c + - 0a5c785ac6db + - 589e7e57fd6d + - 64e2edfe7a2c + - a1a923cd89e8 - dde39ba9c031 + - b28e0cfa7ba1 + - e19bebe96cd2 - 87ee588b3d45 - ce3c7f062223 - - a1a923cd89e8 - - a68aa6c1204a - - e19bebe96cd2 - - 0a5c785ac6db - - b28e0cfa7ba1 - - 64e2edfe7a2c + - 07e8b80f278c - a8eabd2838f6 - - 589e7e57fd6d + - a68aa6c1204a tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/blast.yml b/usegalaxy.org.au/blast.yml index f713f1ea1..604ff9d67 100644 --- a/usegalaxy.org.au/blast.yml +++ b/usegalaxy.org.au/blast.yml @@ -8,30 +8,30 @@ tools: - name: diamond owner: bgruening revisions: - - e8ac2b53f262 + - 62c9df8382c2 - 54f751e413f4 + - e8ac2b53f262 - f921014aba5a - - 62c9df8382c2 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: ncbi_blast_plus owner: devteam revisions: - d999e774072a - - 0e3cf9594bb7 - - 2889433c7ae1 - - cbf3f518b668 - - a52d2d93e595 - - e25d3acf6e68 - - 5edc472ec434 - 6f386c5dc4fb + - e25d3acf6e68 - acf4e47b734c + - a52d2d93e595 + - cbf3f518b668 + - 5edc472ec434 + - 0e3cf9594bb7 + - 2889433c7ae1 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu - name: taxonomy_krona_chart owner: crs4 revisions: - - 1334cb4c6b68 - e9005d1f3cfd + - 1334cb4c6b68 tool_panel_section_label: Blast + tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chemicaltoolbox.yml b/usegalaxy.org.au/chemicaltoolbox.yml index d631d2de7..168ba9496 100644 --- a/usegalaxy.org.au/chemicaltoolbox.yml +++ b/usegalaxy.org.au/chemicaltoolbox.yml @@ -8,13 +8,13 @@ tools: - name: ambertools_acpype owner: chemteam revisions: - - da6bd1975a71 - - 6ca543ec1bf8 - 095ad4d096d1 + - 6ca543ec1bf8 + - da6bd1975a71 - f4230f116196 - - c8cdde00b105 - - 710301bc46fa - 27ee142314a9 + - 710301bc46fa + - c8cdde00b105 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: autodock_vina_prepare_box @@ -92,8 +92,8 @@ tools: - name: ctb_frankenstein_ligand owner: bgruening revisions: - - 8e214e52e461 - 7255688c77f3 + - 8e214e52e461 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: ctb_im_conformers @@ -130,30 +130,30 @@ tools: - name: gmx_editconf owner: chemteam revisions: + - 3b8a9d5ced85 + - 79cfd9ead848 - 88076940fa94 - bfb65cb551d8 - - 79cfd9ead848 - - 3b8a9d5ced85 - 0fac8e2afc13 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_em owner: chemteam revisions: - - f5d979cb4b54 - 55918daa5651 - - d532b7e5f64b + - eb6564a60136 + - f5d979cb4b54 - 715cd0e87781 - b46d4b4d995c - - eb6564a60136 + - d532b7e5f64b tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_energy owner: chemteam revisions: - 5579659312e6 - - dae135dfd519 - fdf2cc80adb5 + - dae135dfd519 - d2f955aea23a - f26afd1b7104 tool_panel_section_label: ChemicalToolBox @@ -161,43 +161,43 @@ tools: - name: gmx_merge_topology_files owner: chemteam revisions: - - bc31d02be922 - d1d0efda35c0 - 319a28774da9 + - bc31d02be922 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_setup owner: chemteam revisions: - ed736e6eee39 + - 2c349b027a01 + - cac1886249a2 - 4da9ee404eab - 070e3ecc3fda - - cac1886249a2 - - 2c349b027a01 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_sim owner: chemteam revisions: - - d1f803b5943c - - da8753545526 - - f197e34c33a9 - - c0c9a5024177 - - 73008ef1f487 - - 807aa4c9293d - 2e219a2d9327 - 525ca7c8065f + - 807aa4c9293d + - f197e34c33a9 + - 73008ef1f487 + - c0c9a5024177 + - da8753545526 + - d1f803b5943c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_solvate owner: chemteam revisions: - - 61094e01eff9 - - 2c8ed1b52bf7 - c4fbab8e03c5 + - 2c8ed1b52bf7 + - 61094e01eff9 + - 27ea4e1a3f95 - 1809414a9454 - 7568ae18908a - - 27ea4e1a3f95 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: gmx_trj @@ -209,11 +209,11 @@ tools: - name: md_converter owner: chemteam revisions: + - 79e8ab8f1e81 - 730ef07b90ae + - d7ec25187599 - ccfbd956a2d3 - ba83f0923369 - - d7ec25187599 - - 79e8ab8f1e81 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: mdanalysis_cosine_analysis @@ -269,9 +269,9 @@ tools: owner: bgruening revisions: - e6011617c748 - - 4242b4d68e9c - e2c36f62e22f - b59c91adeac1 + - 4242b4d68e9c tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: openbabel_remduplicates @@ -283,8 +283,8 @@ tools: - name: openbabel_svg_depiction owner: bgruening revisions: - - 7672039a0bb0 - 75ee9c410951 + - 7672039a0bb0 tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu - name: qcxms_getres @@ -351,9 +351,9 @@ tools: - name: sucos_max_score owner: bgruening revisions: - - 85fad59f8168 - 9b48456a96fe - d4c67ced6abc + - 85fad59f8168 - bf99565cec1f tool_panel_section_label: ChemicalToolBox tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/chip_seq.yml b/usegalaxy.org.au/chip_seq.yml index 557a1b727..90f5c987f 100644 --- a/usegalaxy.org.au/chip_seq.yml +++ b/usegalaxy.org.au/chip_seq.yml @@ -2,10 +2,10 @@ tools: - name: diffbind owner: bgruening revisions: + - 163688bb8f73 - fa56d93f7980 - - c97a786e8fb5 - 2605cbdaa7d8 - - 163688bb8f73 + - c97a786e8fb5 - f907216064f6 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu @@ -25,11 +25,11 @@ tools: - name: macs2 owner: iuc revisions: + - 495a4173006f - 640d3af5d833 + - 86e2413cf3f8 - 424aefbd7777 - f5d67c722d67 - - 495a4173006f - - 86e2413cf3f8 tool_panel_section_label: ChiP-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: rnachipintegrator diff --git a/usegalaxy.org.au/collection_operations.yml b/usegalaxy.org.au/collection_operations.yml index bae34340c..582b71716 100644 --- a/usegalaxy.org.au/collection_operations.yml +++ b/usegalaxy.org.au/collection_operations.yml @@ -10,16 +10,16 @@ tools: owner: nml revisions: - 33151a38533a + - 830961c48e42 - 90981f86000f - 25136a2b0cfe - - 830961c48e42 tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: collection_column_join owner: iuc revisions: - - 3ddd99c7efee - dfde09461b1e + - 3ddd99c7efee tool_panel_section_label: Collection Operations tool_shed_url: toolshed.g2.bx.psu.edu - name: split_file_on_column @@ -31,8 +31,8 @@ tools: - name: split_file_to_collection owner: bgruening revisions: - - 0046692724f9 - 6cbe2f30c2d7 + - 0046692724f9 - 2dae863c8f42 - baabc30154cd tool_panel_section_label: Collection Operations diff --git a/usegalaxy.org.au/convert_formats.yml b/usegalaxy.org.au/convert_formats.yml index 1f1446695..a046d6127 100644 --- a/usegalaxy.org.au/convert_formats.yml +++ b/usegalaxy.org.au/convert_formats.yml @@ -16,32 +16,32 @@ tools: - name: biom_add_metadata owner: iuc revisions: + - ab9350a8ab4d + - 3b6f97e7094c - 6ef0b5664c69 - - 4a6ee918c13a - - 367b1ed91207 - - a3b86937ead6 - 5e1240a87bcb - - 3b6f97e7094c - - e3cbd2287f63 - - ab9350a8ab4d - f3a19509108a - 0b3c3ad92827 + - a3b86937ead6 + - 4a6ee918c13a + - 367b1ed91207 + - e3cbd2287f63 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: biom_convert owner: iuc revisions: - - bd46669113b9 + - d4d4e9febf5c + - e177a8ea0bf1 - e525f9ffb9ac - - 72ed72122deb - 501c21cce614 + - 091bb5922a82 - 1b5fc03380d4 + - 72ed72122deb + - bd46669113b9 + - 33c99804a32f - 54ccb7e1f49a - - d4d4e9febf5c - 584008e574b2 - - e177a8ea0bf1 - - 091bb5922a82 - - 33c99804a32f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: bp_genbank2gff3 @@ -59,24 +59,24 @@ tools: - name: fasta_to_tabular owner: devteam revisions: - - 7e801ab2b70e - e7ed3c310b74 + - 7e801ab2b70e tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_fasta owner: devteam revisions: - - 77b41c89d856 - 8979c288aefb - 186b8d913e6c + - 77b41c89d856 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - - 43807a65369f - 614a63f14adf - 4b347702c4aa + - 43807a65369f tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gfa_to_fa @@ -95,9 +95,9 @@ tools: - name: gffread owner: devteam revisions: - - 3e436657dcd0 - 154d00cbbf2d - 4dea02886337 + - 3e436657dcd0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: gtftobed12 @@ -135,24 +135,25 @@ tools: - name: tabular_to_fastq owner: devteam revisions: - - 78fb18899c99 - 2dcfbbf9071a + - 78fb18899c99 - 68f57cc8fad0 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: thermo_raw_file_converter owner: galaxyp revisions: - - 63769c4217a7 - 26c6706bfb07 - - b9b385097f13 - 92ac8e086317 + - 63769c4217a7 - 19e45916daf9 + - b9b385097f13 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fatovcf owner: iuc revisions: + - a40dd4fd3096 - 3c19c84fbce2 tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu @@ -167,8 +168,8 @@ tools: - name: ucsc_wigtobigwig owner: iuc revisions: - - 98704d357ede - a2f83a375bf2 + - 98704d357ede - fa49730d1d4b tool_panel_section_label: Convert Formats tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/deeptools.yml b/usegalaxy.org.au/deeptools.yml index e63dcfccf..08e1b0cd2 100644 --- a/usegalaxy.org.au/deeptools.yml +++ b/usegalaxy.org.au/deeptools.yml @@ -2,46 +2,46 @@ tools: - name: deeptools_bam_compare owner: bgruening revisions: - - 5f6d123679f4 - 268e91e540ee - - a1ca9bccc7f2 - - c929a006727f - - 29451af70c52 + - 5f6d123679f4 - de72ba3ed6f2 - e821645ef8fc + - 29451af70c52 + - a1ca9bccc7f2 + - c929a006727f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_coverage owner: bgruening revisions: - - 5d11599b8a7d - - bb1e4f63e0e6 - - 0e49b109abc2 - 0e143b4c3987 + - bb1e4f63e0e6 - 7a7fd0f5f15d + - 5d11599b8a7d - 2d2cf5c1ea8a + - 0e49b109abc2 - 12af64f93288 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bam_pe_fragmentsize owner: bgruening revisions: - - 81b1e3e1fc6c + - c06951d10364 - 1d848bc4585f - 7c1beb6d6eca - dc059492a995 - 195e98217334 - - c06951d10364 + - 81b1e3e1fc6c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_bigwig_compare owner: bgruening revisions: - - 07418a30ed01 - - 26e7304d6737 + - 93eb012d9eed - 3d211717a775 - a67ac707496a - - 93eb012d9eed + - 07418a30ed01 + - 26e7304d6737 - 71aa86af6762 - bfff7454b59a tool_panel_section_label: DeepTools @@ -49,158 +49,158 @@ tools: - name: deeptools_compute_gc_bias owner: bgruening revisions: + - 26983857c91a + - dd0b7398bb96 + - 5be24eba848d - 29fcfd36e90a - 2bc10a9ca58b - - 5be24eba848d - b8858746dc1f - - dd0b7398bb96 - 56d5b797ce84 - - 26983857c91a tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix_operations owner: bgruening revisions: - - ee3a1b0f45f1 - - 7ef978dc1b8a + - 7e6bcd2e5128 - c3e012dfe21f - - 72bfafe3330b + - 7ef978dc1b8a - e6d0bff01239 + - 72bfafe3330b + - ee3a1b0f45f1 - 9384cd033f30 - - 7e6bcd2e5128 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_compute_matrix owner: bgruening revisions: - - fd1275e01605 + - d9a637e83828 - 9470f29702f8 - - 167788df3b46 - - a60c359ec43c + - fd1275e01605 - fb9cf9c97ec4 + - a60c359ec43c - b73e213add0c + - 167788df3b46 - 514fa53b5efb - - d9a637e83828 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_correct_gc_bias owner: bgruening revisions: - - c34d11ea4ba6 - 5bffaa8354a1 - - e479c7ca5570 - 2c37ce318bc3 - - ca0616bb2cdf - - a02cfa31e9cb - 86febdcc4283 + - a02cfa31e9cb + - ca0616bb2cdf + - e479c7ca5570 + - c34d11ea4ba6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bam_summary owner: bgruening revisions: - - 01fb6a7654e6 - - 2d466b530754 - - 78f405266706 + - 192ef85c0b0b + - 004aea905d4d - 1fcb7adc39b8 + - 78f405266706 + - 01fb6a7654e6 - 69a8621ca2f0 - - 004aea905d4d - - 192ef85c0b0b + - 2d466b530754 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_multi_bigwig_summary owner: bgruening revisions: - - 9ecba5e225a6 - - d580d6acd1df - - db940c262830 - - 137c4beed34b - d9ce4897dbb2 - - 2f9e4843f480 - 459cfa861f0b - 3c9f0c486cca + - 2f9e4843f480 + - db940c262830 + - d580d6acd1df + - 137c4beed34b + - 9ecba5e225a6 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_correlation owner: bgruening revisions: - - 32e451def88c + - fbe773640707 - bad3ca889618 - - f264afa9fa6f - - fd408d755394 - bd7db9e2f2cb - - fbe773640707 + - fd408d755394 - 2c66e43f1c86 + - f264afa9fa6f + - 32e451def88c tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_coverage owner: bgruening revisions: - - 7e361d147872 - 3b9d990a0a0e + - 4e12ea27f788 + - 7e361d147872 + - 56bce3c82278 - 231994413f89 - 7fda5607e777 - - 56bce3c82278 - - 4e12ea27f788 - 9368fbc49c8b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_enrichment owner: bgruening revisions: + - d9114ef1c8a5 - c03c3384cd81 - - ce4ce3316f74 - 94ca68515826 - - d9114ef1c8a5 - - 4431f39ede55 - - b1779366c8e9 - e65d16fb2724 + - b1779366c8e9 + - ce4ce3316f74 + - 4431f39ede55 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_fingerprint owner: bgruening revisions: - - b88ebb3672a1 - - 4ed32329e0ed + - 793665fff0f8 - f8fc4e5aff9d + - 23f7c5f1fdaf + - 4ed32329e0ed - 2da482e408b8 - d57251071381 - - 793665fff0f8 - - 23f7c5f1fdaf + - b88ebb3672a1 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_heatmap owner: bgruening revisions: - - 010e58e9d822 - - e4c7985d4585 - - a4dfb122e52b - a7849312d328 - - c60570fa602f - 25d830337d31 - - 512155688d98 + - e4c7985d4585 - ba6efa77fb79 + - a4dfb122e52b + - 010e58e9d822 + - 512155688d98 + - c60570fa602f tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_pca owner: bgruening revisions: - - 38e3f226248b - - 69264da0ce77 - - 443d9a9d6d11 - - 4d678170d29b - - c899e0ccff8c - aa200e4f3939 + - c899e0ccff8c - 00d869ea03a1 + - 69264da0ce77 + - 4d678170d29b + - 443d9a9d6d11 + - 38e3f226248b tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu - name: deeptools_plot_profile owner: bgruening revisions: - - aac8444d6681 - 10301d137111 - - d806504e96d9 - a2d70c4fd406 - - 6662b1a8d326 - c361b12d207a + - d806504e96d9 + - 6662b1a8d326 + - aac8444d6681 tool_panel_section_label: DeepTools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/dna_metabarcoding.yml b/usegalaxy.org.au/dna_metabarcoding.yml index 2d0c0d41c..8525c44bf 100644 --- a/usegalaxy.org.au/dna_metabarcoding.yml +++ b/usegalaxy.org.au/dna_metabarcoding.yml @@ -2,15 +2,15 @@ tools: - name: obi_annotate owner: iuc revisions: - - d50dc96e3ce9 - 3021b9f5809f + - d50dc96e3ce9 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_clean owner: iuc revisions: - - 7d16de45c021 - 08d873cdd5f6 + - 7d16de45c021 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_convert @@ -37,8 +37,8 @@ tools: - name: obi_ngsfilter owner: iuc revisions: - - 91a1ed0b486f - 76e69de726b2 + - 91a1ed0b486f tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_sort @@ -51,8 +51,8 @@ tools: - name: obi_stat owner: iuc revisions: - - 5f4544915893 - 39320fee9d70 + - 5f4544915893 tool_panel_section_label: DNA Metabarcoding tool_shed_url: toolshed.g2.bx.psu.edu - name: obi_tab diff --git a/usegalaxy.org.au/emboss.yml b/usegalaxy.org.au/emboss.yml index 42a614fb1..68ea85a08 100644 --- a/usegalaxy.org.au/emboss.yml +++ b/usegalaxy.org.au/emboss.yml @@ -2,9 +2,9 @@ tools: - name: emboss_5 owner: devteam revisions: - - ce385837c160 - - dba489bfcd62 - 832c20329690 + - ce385837c160 - 63dd26468588 + - dba489bfcd62 tool_panel_section_label: EMBOSS tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/epigenetics.yml b/usegalaxy.org.au/epigenetics.yml index 3e90a2b6c..9c6188c78 100644 --- a/usegalaxy.org.au/epigenetics.yml +++ b/usegalaxy.org.au/epigenetics.yml @@ -9,10 +9,10 @@ tools: owner: iuc revisions: - 6da3972210ee - - cf1322aeb137 - - d82648ad25a3 - - 29bdbc353f20 - 62f5fab76dfb + - 29bdbc353f20 + - d82648ad25a3 + - cf1322aeb137 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: metilene @@ -24,7 +24,7 @@ tools: - name: pileometh owner: bgruening revisions: - - d6787bab7b11 - 183cb55b1729 + - d6787bab7b11 tool_panel_section_label: Epigenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastafastq.yml b/usegalaxy.org.au/fastafastq.yml index 7f5e93015..8abdcf54a 100644 --- a/usegalaxy.org.au/fastafastq.yml +++ b/usegalaxy.org.au/fastafastq.yml @@ -8,42 +8,42 @@ tools: - name: cutadapt owner: lparsons revisions: - - e4691e1589d3 - - fe74900d6dc7 - - c053d4cad713 - - 64172f1c1202 + - de6cebe3c043 - 660cffd8d92a - - 5915ea1ec9b1 - 8c0175e03cee - - c5e2e5902201 - - 8665bcc8b847 - - c4b82dce8335 - - 288f97432497 - - 4e5056fefd88 - - 44e2cc14f75b - 135b80fb1ac2 - - de6cebe3c043 - - 5eb7e84243f2 - - 48f587c13075 - b1c926deaa2d + - c053d4cad713 + - 48f587c13075 + - e4691e1589d3 + - 5eb7e84243f2 + - 288f97432497 + - 4e5056fefd88 - 093678460093 + - 44e2cc14f75b + - 5915ea1ec9b1 - 49370cb85f0f + - 8665bcc8b847 + - fe74900d6dc7 + - 64172f1c1202 + - c4b82dce8335 + - c5e2e5902201 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_clipping_histogram owner: devteam revisions: - 9db07fd39f85 - - 8889eb864cef - f666895cbebd + - 8889eb864cef tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - - de2db1bdfbf8 - - 5cbde03c1103 - 7d37cfda8e00 + - 5cbde03c1103 + - de2db1bdfbf8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_concatenate_by_species @@ -61,46 +61,46 @@ tools: - name: fasta_formatter owner: devteam revisions: - - 859422bcb689 - 516b97a23d7e - 9457a20156db + - 859422bcb689 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_merge_files_and_filter_unique_sequences owner: galaxyp revisions: - - f546e7278f04 - 2904d46167da + - f546e7278f04 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_nucleotide_changer owner: devteam revisions: - f773e98b26cf - - f81d4362b6c1 - ec0b5076173a + - f81d4362b6c1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_stats owner: iuc revisions: - - 9c620a950d3a - - cd0874854f51 - - 0dbb995c7d35 - 56022eb50bbd + - 0dbb995c7d35 + - cd0874854f51 + - 9c620a950d3a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastp owner: iuc revisions: - - dbfc505896e9 - - c59d48774d03 - - ecb9f4854617 - 65b93b623c77 - - d60c3f704da0 + - ecb9f4854617 + - dbf9c561ef29 - 1d8fe9bc4cb0 + - dbfc505896e9 + - d60c3f704da0 - a626e8c0e1ba - - dbf9c561ef29 + - c59d48774d03 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_combiner @@ -114,65 +114,65 @@ tools: - name: fastq_filter owner: devteam revisions: - - '144275714590' - 10b75444feae - 81a9090d6df3 + - '144275714590' tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_groomer owner: devteam revisions: - - e9f8633db0a2 - 47e5dbc3e790 - 8611b80a14d6 + - e9f8633db0a2 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_manipulation owner: devteam revisions: - - 7861f3b10c68 - 5b87038565bb - e30352e889fe + - 7861f3b10c68 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_masker_by_quality owner: devteam revisions: + - 4e1d64e6385f - 9dfda4e310ed - 9282652e7234 - - 4e1d64e6385f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: + - 523c2aff0376 - 03d57fea6482 - f3936d0632cb - - 523c2aff0376 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - b41c2c1bcfbf - - 3e396e702cea - 2ccb8dcabddc + - 3e396e702cea tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_joiner owner: devteam revisions: - c885369b207b - - 8d958759cf2a - 09a2199cd356 + - 8d958759cf2a tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_splitter owner: devteam revisions: + - e39cc71d3ed6 - 397dc333436b - 249c8393f2d4 - - e39cc71d3ed6 - 35e38452bb3f tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu @@ -180,16 +180,16 @@ tools: owner: devteam revisions: - 54053ea6c77e - - 045f0e1043f7 - 74db4cffab1f + - 045f0e1043f7 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_stats owner: devteam revisions: - - b1cea1b2fcd0 - - f86c27295151 - f0e7deab6518 + - f86c27295151 + - b1cea1b2fcd0 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer @@ -210,18 +210,18 @@ tools: - name: fastx_artifacts_filter owner: devteam revisions: - - 529bccd5e4a1 - 09070cacefd8 - - d5e9e83cd3d8 - 567d5b3c52b1 + - 529bccd5e4a1 + - d5e9e83cd3d8 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_barcode_splitter owner: devteam revisions: - 8abdedf55101 - - 0b7ec11b3c7c - 4bedca26c133 + - 0b7ec11b3c7c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_clipper @@ -229,43 +229,43 @@ tools: revisions: - 90858c306551 - 736b8f6ee456 - - cb1e251cac37 - bdf1ce174e39 + - cb1e251cac37 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_collapser owner: devteam revisions: - 7ce1891db6f5 - - 421f0af4ee95 - 07497255281e + - 421f0af4ee95 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - - 3599f5451ee2 - - b29d37ca9e41 - 02f8a17a4ebd + - b29d37ca9e41 + - 3599f5451ee2 - f984bb114520 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - - 0c2907307ba4 - - 177f0621c266 - 6027ef51ef91 + - 177f0621c266 - e246088b6e34 + - 0c2907307ba4 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - - 547e8d00f11c - - 377ac2829eac - - 61b4cedc8934 - 73194cdd4f57 + - 61b4cedc8934 + - 377ac2829eac + - 547e8d00f11c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiadapterfilt @@ -278,9 +278,9 @@ tools: owner: iuc revisions: - 037f0acc7830 - - 2f804526f5fd - - f69501361cec - b4c6f054210a + - f69501361cec + - 2f804526f5fd tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seq_select_by_id @@ -293,17 +293,17 @@ tools: - name: seqkit_sort owner: iuc revisions: + - fdc21382376d - 29ef2c5ec205 - 61eb4cfc7313 - - fdc21382376d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - - 812705bcf39c - - fe1ae2ebf63d - 795cd16de38f + - fe1ae2ebf63d + - 812705bcf39c tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk @@ -317,47 +317,47 @@ tools: - name: trimmomatic owner: pjbriggs revisions: - - 51b771646466 - dfa082f84068 + - 51b771646466 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - - d3f58a0dc09d - bf04bd405d5b - 71f649c23021 + - d3f58a0dc09d tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_count owner: iuc revisions: - - 71ad4a56c40c - - b557acca0b56 - - 8250ea3a1501 - - a535cf1e5da4 - 24013bf85a6f - e654095ab143 + - 71ad4a56c40c + - a535cf1e5da4 + - 8250ea3a1501 + - b557acca0b56 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_dedup owner: iuc revisions: - - c5a2ee07c4e1 - f1d33e4c7bd8 + - c5a2ee07c4e1 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_extract owner: iuc revisions: - - 7a7e33d28f62 - 6a675c3aa610 - - 7accf7407811 - 27ac32a22ad2 + - 9fa7803d1c51 + - 7a7e33d28f62 - f3759eec3018 + - 7accf7407811 - 828dba98cdb4 - 015cf18f4a15 - - 9fa7803d1c51 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu - name: umi_tools_group @@ -371,7 +371,7 @@ tools: owner: iuc revisions: - e4e12f0b3af1 - - 953b4821b183 - 4c8a1c7d3608 + - 953b4821b183 tool_panel_section_label: FASTA/FASTQ tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fastq_quality_control.yml b/usegalaxy.org.au/fastq_quality_control.yml index a6ba2d6ce..67b483ffa 100644 --- a/usegalaxy.org.au/fastq_quality_control.yml +++ b/usegalaxy.org.au/fastq_quality_control.yml @@ -2,54 +2,54 @@ tools: - name: fastq_quality_filter owner: devteam revisions: - - ce9cd02d5b88 - 64e9a6afdd0c - - e41385662e5e - 7b4468117008 + - e41385662e5e + - ce9cd02d5b88 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_trimmer_by_quality owner: devteam revisions: - - c64d534a763c - 8050e091e99b + - c64d534a763c tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqc owner: devteam revisions: - - 5ec9f6bceaee - - f2e8552cf1d0 - - ff9530579d1f - - 2c64fded1286 - - e7b2202befea - 9da02be9c6cc + - ff9530579d1f - 3d0c7bdf12f5 + - 5ec9f6bceaee - 2b0c9d9fc6ca + - 2c64fded1286 + - e7b2202befea + - f2e8552cf1d0 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqe owner: iuc revisions: + - c1a33f603da2 - 89d299153577 - a252d8415583 - - c1a33f603da2 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_nucleotides_distribution owner: devteam revisions: - - b6b54ba71bd8 - 18a51655db17 + - b6b54ba71bd8 - ad116ae3f4d9 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_quality_statistics owner: devteam revisions: - - cc0fd298cc17 - - 7306ec78632a - 59003d0543cd + - 7306ec78632a + - cc0fd298cc17 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: filtlong @@ -63,23 +63,23 @@ tools: - name: multiqc owner: iuc revisions: - - 5e33b465d8d5 - 75c93c70d094 - - c1a4b5f3b432 - - 9a913cdee30e - - 3d93dd18d9f8 - - bf675f34b056 - b2f1f75d49c4 - - f7e2f1eb3a16 + - c1a4b5f3b432 - abfd8a6544d7 - 1c2db0054039 + - bf675f34b056 + - 3d93dd18d9f8 + - 5e33b465d8d5 + - 9a913cdee30e + - f7e2f1eb3a16 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - - 084bbd8ba7b8 - - cd7e644cae1d - 949f01671246 + - cd7e644cae1d + - 084bbd8ba7b8 tool_panel_section_label: FASTQ Quality Control tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/fetch_alignmentssequences.yml b/usegalaxy.org.au/fetch_alignmentssequences.yml index 0dfc5355c..c01999d90 100644 --- a/usegalaxy.org.au/fetch_alignmentssequences.yml +++ b/usegalaxy.org.au/fetch_alignmentssequences.yml @@ -8,7 +8,7 @@ tools: - name: isescan owner: iuc revisions: - - 19f42b3ea391 - 9e776e7fab4f + - 19f42b3ea391 tool_panel_section_label: Fetch Alignments/Sequences tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/filter_and_sort.yml b/usegalaxy.org.au/filter_and_sort.yml index 1545a9f2d..b747339b5 100644 --- a/usegalaxy.org.au/filter_and_sort.yml +++ b/usegalaxy.org.au/filter_and_sort.yml @@ -2,8 +2,8 @@ tools: - name: filter_by_fasta_ids owner: galaxyp revisions: - - dff7df6fcab5 - 3c623e81be77 + - dff7df6fcab5 tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu - name: sample_seqs @@ -16,8 +16,8 @@ tools: - name: seq_filter_by_id owner: peterjc revisions: + - 83a19df00eab - 141612f8c3e3 - 85ef5f5a0562 - - 83a19df00eab tool_panel_section_label: Filter and Sort tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/gemini_tools.yml b/usegalaxy.org.au/gemini_tools.yml index d90b0a808..6585da8c3 100644 --- a/usegalaxy.org.au/gemini_tools.yml +++ b/usegalaxy.org.au/gemini_tools.yml @@ -9,23 +9,23 @@ tools: - name: gemini_amend owner: iuc revisions: - - be828b79bd4d - 4bd4870ecd33 + - be828b79bd4d tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_annotate owner: iuc revisions: + - 0c8f7322f8fc - 8f53b238a360 - f2f3bc622a16 - - 0c8f7322f8fc tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_burden owner: iuc revisions: - - df57188562f0 - 1a4c5adcd587 + - df57188562f0 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_comp_hets @@ -38,8 +38,8 @@ tools: - name: gemini_db_info owner: iuc revisions: - - 7d75673f4d6f - 4c5f4e9b1931 + - 7d75673f4d6f tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_de_novo @@ -52,8 +52,8 @@ tools: - name: gemini_dump owner: iuc revisions: - - 40f85b45e472 - 96a2d270bf0f + - 40f85b45e472 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_fusions @@ -66,8 +66,8 @@ tools: - name: gemini_gene_wise owner: iuc revisions: - - d46017ddbf94 - 452104bdc655 + - d46017ddbf94 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_inheritance @@ -87,8 +87,8 @@ tools: owner: iuc revisions: - cf61daf064fe - - 45296e47d565 - b2c25142267e + - 45296e47d565 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_lof_sieve @@ -108,8 +108,8 @@ tools: - name: gemini_pathways owner: iuc revisions: - - 6b09debcfc49 - 9199331c3421 + - 6b09debcfc49 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_qc @@ -122,9 +122,9 @@ tools: - name: gemini_query owner: iuc revisions: + - 840fb4850be3 - da74170c55c7 - 666f60a9331a - - 840fb4850be3 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu - name: gemini_recessive_and_dominant @@ -165,7 +165,7 @@ tools: - name: gemini_windower owner: iuc revisions: - - 0c58ba91d018 - 8f04952b8882 + - 0c58ba91d018 tool_panel_section_label: Gemini Tools tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/genome_editing.yml b/usegalaxy.org.au/genome_editing.yml index 061f295f2..301093442 100644 --- a/usegalaxy.org.au/genome_editing.yml +++ b/usegalaxy.org.au/genome_editing.yml @@ -9,28 +9,28 @@ tools: - name: mageck_gsea owner: iuc revisions: - - b946929d31c4 - d46e36492bff + - b946929d31c4 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_mle owner: iuc revisions: - - b36c85e37a48 - 26126538a86f + - b36c85e37a48 tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_pathway owner: iuc revisions: - - 9744e1124d0f - 39a996d44e16 + - 9744e1124d0f tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu - name: mageck_test owner: iuc revisions: - - 9b4f4533c9ee - 688a8eccea71 + - 9b4f4533c9ee tool_panel_section_label: Genome Editing tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/get_data.yml b/usegalaxy.org.au/get_data.yml index 21b103b41..72075d30f 100644 --- a/usegalaxy.org.au/get_data.yml +++ b/usegalaxy.org.au/get_data.yml @@ -2,10 +2,10 @@ tools: - name: dbbuilder owner: galaxyp revisions: - - b39347891609 - - 983bf725dfc2 - c1b437242fee - e9df53a75f3c + - 983bf725dfc2 + - b39347891609 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ega_download_client @@ -17,54 +17,54 @@ tools: - name: ncbi_acc_download owner: iuc revisions: - - e063168e0a81 - 28587613264f + - e063168e0a81 - 1c58de56d587 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: sra_tools owner: iuc revisions: - - 4df8de2d0e48 - - 6ea73833cf67 + - e407b9da183a - 516a54ddf218 - - 8848455c0270 - - 653e89d73fc4 - - 69ebb7f46e45 - - aad3885b3216 - - 1790dcf3c32d - - 4317d3cb6cba + - c441583adae5 - ba931a59dd59 + - 6591f049cf7e + - 6ea73833cf67 + - e08a7ad4378b + - 69ebb7f46e45 + - 653e89d73fc4 - 83c7d564b128 + - 4df8de2d0e48 - 734abc7ac21d - - e08a7ad4378b - - c441583adae5 - - 9a776b080193 + - 4317d3cb6cba + - 8848455c0270 - f8054ea1c365 - - f5ea3ce9b9b0 - 7068f48d0ef9 - - 5e6237d58b0c + - f5ea3ce9b9b0 - 1ec814014652 - - 6591f049cf7e - - e407b9da183a + - 1790dcf3c32d + - 5e6237d58b0c + - aad3885b3216 + - 9a776b080193 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: unipept owner: galaxyp revisions: - 21a560af5913 + - 9aaa46d45472 - 34758ab8aaa4 - 75b3b3d0adbf - - 9aaa46d45472 tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu - name: uniprot_rest_interface owner: bgruening revisions: - af5eccf83605 - - bfdc6a7ffd3a - 054483e27a35 - - 468c71dac78a - 95fb5712344f + - bfdc6a7ffd3a + - 468c71dac78a tool_panel_section_label: Get Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/graphdisplay_data.yml b/usegalaxy.org.au/graphdisplay_data.yml index 9663756ba..ce0237132 100644 --- a/usegalaxy.org.au/graphdisplay_data.yml +++ b/usegalaxy.org.au/graphdisplay_data.yml @@ -2,15 +2,15 @@ tools: - name: circos owner: iuc revisions: - - 7f13dc906cb9 - - a64dc31ab7f2 - - 4b519282a05b - - df7356989ac1 - - 290a11559985 - 740057a5126d + - 290a11559985 + - a64dc31ab7f2 + - c4bde687c846 + - 7f13dc906cb9 - fd59d783248a - ae9994cf526f - - c4bde687c846 + - 4b519282a05b + - df7356989ac1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: draw_stacked_barplots @@ -28,9 +28,9 @@ tools: - name: fastq_quality_boxplot owner: devteam revisions: - - 7cf5b1d072b5 - - 867ab348287d - f95284aa2946 + - 867ab348287d + - 7cf5b1d072b5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: geneiobio @@ -42,24 +42,24 @@ tools: - name: ggplot2_heatmap2 owner: iuc revisions: - - 3b37b1b1c3a7 - - ca7cb0eaad62 - - '566197475670' - 51c6ccaace7e - - 48b42ee61bc5 - - 53460afd5115 - 374e9062d874 + - '566197475670' + - 3b37b1b1c3a7 + - 53460afd5115 + - 48b42ee61bc5 + - ca7cb0eaad62 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: + - da4c086cff5b - 391a4cc45fea - 3d059e9c2fba - - 1a72f938213e - 10515715c940 - - da4c086cff5b - d3a9e32672ec + - 1a72f938213e tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram @@ -72,26 +72,26 @@ tools: - name: ggplot2_pca owner: iuc revisions: - - b1268b7544d3 - ae344ccf9d62 + - b1268b7544d3 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - - 1acf88921176 - - 5fe1dc76176e - e3a675da7fd0 - 5298e06f14f9 - d0fc8b746d57 + - 5fe1dc76176e - 299307abd804 + - 1acf88921176 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - - 0e7290688b50 - 17b666467c32 + - 0e7290688b50 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: gmaj @@ -103,8 +103,8 @@ tools: - name: graphlan_annotate owner: iuc revisions: - - 97e3b735ed22 - 5d6f8f0bef7c + - 97e3b735ed22 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: graphlan @@ -129,17 +129,17 @@ tools: - name: jbrowse owner: iuc revisions: + - 17359b808b01 + - 6cd09d7b5f37 - fd5dbf0f732e - 4542035c1075 - - 1cfc579079a6 - 667e17248bfe - - 6cd09d7b5f37 + - ca2def38369c + - 1cfc579079a6 - 2bb2e07a7a21 + - 112eb40ba6cf - a6e57ff585c0 - - 17359b808b01 - - ca2def38369c - 836d1aa3e89a - - 112eb40ba6cf tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text @@ -157,31 +157,31 @@ tools: - name: pathview owner: iuc revisions: + - f1691de443a7 - 03c13085aecc - fe154a7af404 - - f1691de443a7 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: pe_histogram owner: iuc revisions: - - 594b85e4237a - bd1416eea1f0 + - 594b85e4237a tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plot_ragtag_paf owner: galaxy-australia revisions: - - c1bed78b9ed5 - 501dcf66c0ce + - c1bed78b9ed5 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: plotly_ml_performance_plots owner: bgruening revisions: - - 85da91bbdbfb - - 62e3a4e8c54c - f234e2e59d76 + - 62e3a4e8c54c + - 85da91bbdbfb - 1c5dcef5ce0f tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu @@ -201,10 +201,10 @@ tools: - name: pretext_snapshot owner: iuc revisions: - - 44c66e8d21e6 + - 26f2fe7e53a1 - 7c9417381ad5 + - 44c66e8d21e6 - 6c571966cfb9 - - 26f2fe7e53a1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: prop_venn @@ -216,14 +216,14 @@ tools: - name: pygenometracks owner: iuc revisions: - - 36b848d5f3ec + - 7dd841a32245 + - 4ac4e7083b7e - 360df4999907 - - 14e7c35f3d00 - a1abfa420d9d - - 4ac4e7083b7e - - 7dd841a32245 - - 326a3db8d9d1 - 2824d77cd8f8 + - 14e7c35f3d00 + - 36b848d5f3ec + - 326a3db8d9d1 tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: volcanoplot @@ -231,8 +231,8 @@ tools: revisions: - 73b8cb5bddcd - 83c573f2e73c - - 44608d0193ed - 2f557f6abbfb + - 44608d0193ed tool_panel_section_label: Graph/Display Data tool_shed_url: toolshed.g2.bx.psu.edu - name: weblogo3 diff --git a/usegalaxy.org.au/hca_single_cell.yml b/usegalaxy.org.au/hca_single_cell.yml index 1661eb404..bee7d4c4c 100644 --- a/usegalaxy.org.au/hca_single_cell.yml +++ b/usegalaxy.org.au/hca_single_cell.yml @@ -21,8 +21,8 @@ tools: - name: salmon_kallisto_mtx_to_10x owner: ebi-gxa revisions: - - 88f5a0a6a818 - e42c217a450f + - 88f5a0a6a818 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_compute_graph @@ -49,22 +49,22 @@ tools: - name: scanpy_find_cluster owner: ebi-gxa revisions: - - 36735850e461 - fc4b3b46dc9d + - 36735850e461 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_markers owner: ebi-gxa revisions: - - 0a8e527d1517 - d8f5224005bb + - 0a8e527d1517 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_find_variable_genes owner: ebi-gxa revisions: - - 64dd8bb151e1 - 79da59a0b180 + - 64dd8bb151e1 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_bbknn @@ -77,30 +77,30 @@ tools: - name: scanpy_integrate_combat owner: ebi-gxa revisions: - - 3c47bc560688 - 352cdf3b2f75 + - 3c47bc560688 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_harmony owner: ebi-gxa revisions: - - c354af93f567 - 6903bc865d63 + - c354af93f567 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_integrate_mnn owner: ebi-gxa revisions: - - 94697510d55f - 9a2f72d7dbd2 + - 94697510d55f - ff6decc0f432 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_multiplet_scrublet owner: ebi-gxa revisions: - - 53ce0e336840 - 70cb0596ffef + - 53ce0e336840 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalise_data @@ -113,15 +113,15 @@ tools: - name: scanpy_parameter_iterator owner: ebi-gxa revisions: - - 0387a2179f88 - 73d43034c860 + - 0387a2179f88 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_embed owner: ebi-gxa revisions: - - 7d5c97823f8b - 1be0fc4d8654 + - 7d5c97823f8b tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot_scrublet @@ -134,15 +134,15 @@ tools: - name: scanpy_plot_trajectory owner: ebi-gxa revisions: - - d3df472a21dc - cb1992d1804b + - d3df472a21dc tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_read_10x owner: ebi-gxa revisions: - - 078aa23c9374 - 287503c35cb4 + - 078aa23c9374 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_regress_variable @@ -155,8 +155,8 @@ tools: - name: scanpy_run_diffmap owner: ebi-gxa revisions: - - 79cc06a557b0 - 6a6364b488db + - 79cc06a557b0 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_dpt @@ -183,8 +183,8 @@ tools: - name: scanpy_run_pca owner: ebi-gxa revisions: - - 0cf90e01d9f8 - 4428dba93375 + - 0cf90e01d9f8 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_run_tsne @@ -197,15 +197,15 @@ tools: - name: scanpy_run_umap owner: ebi-gxa revisions: - - 0f98603d0116 - - ea91cfd0444e - 767a675b5254 + - ea91cfd0444e + - 0f98603d0116 tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_scale_data owner: ebi-gxa revisions: - - e2d0dc8a50ca - 4cc9362782b4 + - e2d0dc8a50ca tool_panel_section_label: HCA Single-cell tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/hicexplorer.yml b/usegalaxy.org.au/hicexplorer.yml index c67fb63bf..47a721f7b 100644 --- a/usegalaxy.org.au/hicexplorer.yml +++ b/usegalaxy.org.au/hicexplorer.yml @@ -2,56 +2,56 @@ tools: - name: hicexplorer_hicbuildmatrix owner: bgruening revisions: - - 9edf8894a22d - - 29f66c353bcb - 0f611e7d7858 - - a4c13ddcc8ee + - 9edf8894a22d - 921a2da49a0c - ed2cca6b5de4 + - a4c13ddcc8ee + - 29f66c353bcb tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindtads owner: bgruening revisions: - - 755df866ad0c - d404277cc87a - - 5746d61f0a91 - - 78fb5e286609 + - 755df866ad0c - ec4b948dc6f0 - 11de0d28ab30 + - 78fb5e286609 + - 5746d61f0a91 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergematrixbins owner: bgruening revisions: - - 4d511437b1e5 + - 03dd3c16ae4e + - f72063d9426b - 9e357a8b2ec3 - 977dc15add20 + - 4d511437b1e5 - 11fa44ee0603 - - 03dd3c16ae4e - - f72063d9426b tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicpca owner: bgruening revisions: - - 3b5b54ed6392 - - 41dbf4d162a2 - - 1da5f169b491 - 0ba4f56a3613 - - 77919cc3618e - c3e5e2cf12b7 + - 77919cc3618e + - 1da5f169b491 + - 41dbf4d162a2 + - 3b5b54ed6392 tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotmatrix owner: bgruening revisions: - - 9939786dd9c9 + - 7babd8a46fe0 - f741330d4a71 - 5308ca68ef3d - - 7babd8a46fe0 - - 12d51d7be66f + - 9939786dd9c9 - b63363075c2e + - 12d51d7be66f tool_panel_section_label: HiCExplorer tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplottads diff --git a/usegalaxy.org.au/imaging.yml b/usegalaxy.org.au/imaging.yml index bc8cc7135..129618979 100644 --- a/usegalaxy.org.au/imaging.yml +++ b/usegalaxy.org.au/imaging.yml @@ -2,19 +2,19 @@ tools: - name: 2d_auto_threshold owner: imgteam revisions: + - 81f0cbca04a7 - 699a5e9146b3 - 8bccb36e055a - 0c777d708acc - - 3df9f0a4bf34 - 7db4fc31dbee - - 81f0cbca04a7 + - 3df9f0a4bf34 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_feature_extraction owner: imgteam revisions: - - 5bc8cdc17fd0 - 5791a7f65275 + - 5bc8cdc17fd0 - 2436a8807ad1 - 0a53256b48c6 tool_panel_section_label: Imaging @@ -31,16 +31,16 @@ tools: owner: imgteam revisions: - 70316d792fc9 - - b1c2c210813c - 77f7159d775a + - b1c2c210813c tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_simple_filter owner: imgteam revisions: - - dba87c4b32d3 - - f70b215d155c - d51310ab328a + - f70b215d155c + - dba87c4b32d3 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: 2d_split_binaryimage_by_watershed @@ -53,33 +53,33 @@ tools: owner: imgteam revisions: - f3360fbeda64 + - fcadded98e61 - 10eed33aa9b2 - b07f4839ca77 - 85edbb7a436b - - fcadded98e61 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: binary2labelimage owner: imgteam revisions: - - 6e65fd971e13 - 984358e43242 + - 6e65fd971e13 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: count_objects owner: imgteam revisions: - - 5bf8eb50b280 - b58447a2eed2 + - 5bf8eb50b280 - 664232d2a3f7 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_cellprofiler owner: bgruening revisions: + - eb6c08714244 - 0e4dccaafef5 - e917a2424690 - - eb6c08714244 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_color_to_gray @@ -108,32 +108,32 @@ tools: - name: cp_display_data_on_image owner: bgruening revisions: - - 5d28ac336861 - 2484086dee41 + - 5d28ac336861 - 6a7da2e5f696 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_enhance_or_suppress_features owner: bgruening revisions: - - f2ed92b011a9 - 11f177b1a59e - bace5a93a97c + - f2ed92b011a9 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_export_to_spreadsheet owner: bgruening revisions: - - d0178bdcd00e - f8fa0f6718a3 - f24c370e5ea4 + - d0178bdcd00e tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_gray_to_color owner: bgruening revisions: - - 31d195bedf6d - 3245681b2f6d + - 31d195bedf6d - ad271f78a87a tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -141,31 +141,31 @@ tools: owner: bgruening revisions: - 993faa34333b - - b6eec6087271 - 87d4d92d7487 + - b6eec6087271 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_image_math owner: bgruening revisions: - - c09dcda1143f - - ff1a86a87364 - 6100a22bf4f2 + - ff1a86a87364 + - c09dcda1143f tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_mask_image owner: bgruening revisions: - - 667a513e67e4 - 3a05117669cf - b178453ea8d1 + - 667a513e67e4 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_granularity owner: bgruening revisions: - - 2564f461de62 - ac5bea85a391 + - 2564f461de62 - a1a961c46d4b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -173,47 +173,47 @@ tools: owner: bgruening revisions: - 20dbb1f7ec7b - - 91e03287f285 - a32c3f810ade + - 91e03287f285 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_intensity owner: bgruening revisions: - 5499dc6f8ac1 - - 8536b1ae0254 - b64af54c5c09 + - 8536b1ae0254 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_image_quality owner: bgruening revisions: - - e972e07c7845 - 6f4715b8540a + - e972e07c7845 - d3890df07463 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_intensity owner: bgruening revisions: + - 980aed9e8fd5 - 407925835dd9 - e52c75a28c4b - - 980aed9e8fd5 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_object_size_shape owner: bgruening revisions: - - d85f11570109 - 79e10d12d90a - acf3aa487283 + - d85f11570109 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_measure_texture owner: bgruening revisions: - - b76841ee5560 - 035a58c7f54a + - b76841ee5560 - 80b200ae516b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu @@ -227,17 +227,17 @@ tools: - name: cp_relate_objects owner: bgruening revisions: + - 48102a685037 - 8083a87d2fdf - 3a3033222f61 - - 48102a685037 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_save_images owner: bgruening revisions: - 33f4fa1413fb - - 4ecf93628f97 - 27edbb90ab2b + - 4ecf93628f97 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: cp_tile @@ -249,8 +249,8 @@ tools: - name: cp_track_objects owner: bgruening revisions: - - 1fd453cd757b - 972d2c365739 + - 1fd453cd757b tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: idr_download_by_ids @@ -263,15 +263,15 @@ tools: - name: image_info owner: imgteam revisions: - - 7b6d9412c7f8 - - 236ec78b2e53 - f8b4eada923c + - 236ec78b2e53 + - 7b6d9412c7f8 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu - name: overlay_images owner: imgteam revisions: - - 8dc02c854048 - ca362a9bfa20 + - 8dc02c854048 tool_panel_section_label: Imaging tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/ivar.yml b/usegalaxy.org.au/ivar.yml index ce5e53638..4e8a2470c 100644 --- a/usegalaxy.org.au/ivar.yml +++ b/usegalaxy.org.au/ivar.yml @@ -2,93 +2,93 @@ tools: - name: ivar_consensus owner: iuc revisions: - - 78bbd17d0703 - 3e4f434a69c6 + - 40737febe339 + - 3a72fede57ce - e319b5b65879 - f362150bef41 - - e4ee04da1c19 - - 3a72fede57ce + - 78bbd17d0703 - a38934e303b9 - - 40737febe339 - 1069f6db0a0e + - e4ee04da1c19 - d6e72da3ec35 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_filtervariants owner: iuc revisions: - - 0135f1d487a0 + - 2b95d5c04908 + - f91cfb73d369 + - c88553ec696e - 9537184d421f - fcbeda41d0ac - - 618297d23022 - - c88553ec696e - 8f8df367470d - - 7fe36019c073 - - 2b95d5c04908 - - f91cfb73d369 - 72ddd32392cd + - 0135f1d487a0 + - 7fe36019c073 + - 618297d23022 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_getmasked owner: iuc revisions: - - d7e79eb3bcb3 - - fafb3d685fa9 - 2cf4a1cafc16 + - d7e79eb3bcb3 - ad0dc9f4c9e2 + - fafb3d685fa9 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_removereads owner: iuc revisions: - - 8c05afb547fa - - bd2a7d1316b9 - - 3d18f8c3c0f6 - - ee29337f905c - - 5dc33613c288 - - ee2beb764a7b - 94df24c6bc00 + - ee29337f905c + - bd2a7d1316b9 + - 8c05afb547fa - a1c2aecd7a0d - - 28a6f1908fcc + - 43aac8d29685 + - 9eaadf03e0df + - ee2beb764a7b + - 8d36959b000d + - 5dc33613c288 - 6a1515bb0687 + - 3d18f8c3c0f6 + - 28a6f1908fcc - 7f1cfa4c0e32 - - 8d36959b000d - - 9eaadf03e0df - - 43aac8d29685 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_trim owner: iuc revisions: + - d37ede8589b2 - e3bb03cf207a - - 364f4ffec275 - - a250929be21b + - 9f978da6528a - c092052ed673 - - db536ad45f28 + - 86a20ae274fc - cb903c9dc33d + - bcaa0d571ce2 - 5671e1d3d5ee + - 364f4ffec275 + - a250929be21b + - db536ad45f28 - 5d6ed46cc101 - - 86a20ae274fc - 8858fa037a15 - - 9f978da6528a - - bcaa0d571ce2 - - d37ede8589b2 tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu - name: ivar_variants owner: iuc revisions: - - c5c9f02b6167 - - abbc8041e8ec - - f95f403841ad + - 584beffa972b + - 194e3ceee923 - e1a015876aa9 - - 3b6a16d82c1b + - 12d66d0d05ac - 38b91a3190cd + - c5c9f02b6167 + - abbc8041e8ec - 230b05597996 - 49236b03e4fd - - 12d66d0d05ac - ed28dd32141c - - 194e3ceee923 - - 584beffa972b + - f95f403841ad + - 3b6a16d82c1b tool_panel_section_label: iVar tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/join_subtract_and_group.yml b/usegalaxy.org.au/join_subtract_and_group.yml index b346142a2..89d47c9e1 100644 --- a/usegalaxy.org.au/join_subtract_and_group.yml +++ b/usegalaxy.org.au/join_subtract_and_group.yml @@ -2,19 +2,19 @@ tools: - name: datamash_reverse owner: iuc revisions: - - b8a457820315 - 0f1724dd59d2 - - 17e3b698dd52 - f198773344e4 + - b8a457820315 + - 17e3b698dd52 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu - name: datamash_transpose owner: iuc revisions: - 374cb875d38a - - ac092723240d - - 22c2a1ac7ae3 - ba0c40780ecf + - ac092723240d - a513e3fbb4c5 + - 22c2a1ac7ae3 tool_panel_section_label: Join, Subtract and Group tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/machine_learning.yml b/usegalaxy.org.au/machine_learning.yml index e61d24cc2..c018fb0b0 100644 --- a/usegalaxy.org.au/machine_learning.yml +++ b/usegalaxy.org.au/machine_learning.yml @@ -10,91 +10,91 @@ tools: - name: keras_model_config owner: bgruening revisions: - - f22a9297440f - 8a794e6d3388 - 4d81e3e2fb63 + - f22a9297440f tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: keras_train_and_eval owner: bgruening revisions: - - f1b9a42d6809 - e1317b5502fa - 818f9b69d8a0 - b6ef6d0cb6b7 - 2af1346e68c9 + - f1b9a42d6809 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: ml_visualization_ex owner: bgruening revisions: - - c80db5d6fd8c - - 1588f9076e32 + - 05143043ca13 - 8334dc98c48e - 947c2eacccb8 - - 05143043ca13 + - 1588f9076e32 + - c80db5d6fd8c tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: model_prediction owner: bgruening revisions: - 9991c4ddde14 - - 29e4122c90de - - 1552b8cb4a94 - 83228baae3c5 - 25b46af53232 + - 29e4122c90de + - 1552b8cb4a94 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_ensemble owner: bgruening revisions: - - 1a53edc4b438 - - 060ca94ac049 - - 53616c8b0865 + - a07ab242b0b5 - f3dfa4bdf87e - 841a6cc5fc58 - - a07ab242b0b5 + - 1a53edc4b438 + - 53616c8b0865 + - 060ca94ac049 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_generalized_linear owner: bgruening revisions: - 91c4e3331208 - - d4808d5b83da - - dc4b5fd604a6 + - 927586a18553 - 2fc89dcd41c8 + - d4808d5b83da - 40f4447733b2 - - 927586a18553 + - dc4b5fd604a6 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_searchcv owner: bgruening revisions: - - 7626ea9c2e1b - - 301e07345c93 + - 36e8d6d5d01b - e5a5ad882f1f - - 25ab6b4e376e - c6ae57f774c6 - - 36e8d6d5d01b + - 25ab6b4e376e + - 301e07345c93 + - 7626ea9c2e1b tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_svm_classifier owner: bgruening revisions: - 80852884053f - - f9639b488779 + - 4ed102b922cb - 02d2be90dedb - b7c3e9a3b954 + - f9639b488779 - 0630258dcf35 - - 4ed102b922cb tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_to_categorical owner: bgruening revisions: - 14180f9c831e - - 61634a87efc7 - - caeb57858702 - ec69cbe34b73 + - caeb57858702 + - 61634a87efc7 tool_panel_section_label: Machine Learning tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mapping.yml b/usegalaxy.org.au/mapping.yml index 8bfc99abe..cebe8d577 100644 --- a/usegalaxy.org.au/mapping.yml +++ b/usegalaxy.org.au/mapping.yml @@ -2,17 +2,17 @@ tools: - name: bowtie2 owner: devteam revisions: - - 749c918495f7 - - d5ceb9f3c25b - - a6d65b0c67af - - 017aba02828d - 17062a0decb7 - - f6877ad76b00 - - 0d4acadabb04 - 3ba8d4563129 + - 0d4acadabb04 + - f6877ad76b00 + - 017aba02828d + - 749c918495f7 + - 03e9b2fbc005 - cd659e8cc5fa + - d5ceb9f3c25b - 937aa69e715f - - 03e9b2fbc005 + - a6d65b0c67af tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bowtie_wrappers @@ -24,19 +24,19 @@ tools: - name: bwa_mem2 owner: iuc revisions: - - b4a22d90cce9 - bfaa0d22c2e4 + - b4a22d90cce9 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: bwa owner: devteam revisions: - 64f11cf59c6e - - e188dc7a68e6 - - 3fe632431b68 - 53646aaaafef - 2477830927ec - dfd8b7f78c37 + - 3fe632431b68 + - e188dc7a68e6 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: lastz_paired_reads @@ -49,8 +49,8 @@ tools: owner: devteam revisions: - 3e1ea2facca6 - - e7f19d6a9af8 - 37b497aa133f + - e7f19d6a9af8 - 2ff111fac1d7 - 60afcc2c1d05 tool_panel_section_label: Mapping @@ -58,36 +58,36 @@ tools: - name: minimap2 owner: iuc revisions: - - 11a0d50a54e6 - - c0c2d0941de8 + - f54f5baedfdd - b3eab4b67562 - - be1d967337e4 + - 11a0d50a54e6 - 6b1e195506a3 - - 5cc34c3f440d + - 77b2770508f6 + - be1d967337e4 - 09b53c1d4ab1 - - f54f5baedfdd - 037c6e54df11 + - c0c2d0941de8 + - 53c0b7a1a0c3 - 8c6cd2650d1f - - 77b2770508f6 - 3f4d6399997b - - 53c0b7a1a0c3 + - 5cc34c3f440d tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: rna_starsolo owner: iuc revisions: + - 178bdbdb6d24 + - b8f5f6e87f5c - e403d27e8f24 - - 5ef7ec16b04f - - 00fbfac99d39 + - 42ce70172b72 - 1cd2511a396e - - ec9cbd6b9a49 - 45795f582ae9 - - b8f5f6e87f5c - - 9ee34ba73ebf - 13022c3d3076 + - 5ef7ec16b04f - 79b885ce78d7 - - 178bdbdb6d24 - - 42ce70172b72 + - 00fbfac99d39 + - 9ee34ba73ebf + - ec9cbd6b9a49 tool_panel_section_label: Mapping tool_shed_url: toolshed.g2.bx.psu.edu - name: star_fusion diff --git a/usegalaxy.org.au/metabolomics.yml b/usegalaxy.org.au/metabolomics.yml index 09d1b9ad5..db5cef7e9 100644 --- a/usegalaxy.org.au/metabolomics.yml +++ b/usegalaxy.org.au/metabolomics.yml @@ -57,8 +57,8 @@ tools: - name: isolib owner: recetox revisions: - - 2b1118bce0b1 - 6b0fef8a77c0 + - 2b1118bce0b1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: lcmsmatching @@ -76,22 +76,22 @@ tools: - name: matchms_convert owner: recetox revisions: - - b9cc12600553 - 9e83636da9d3 + - b9cc12600553 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_filtering owner: recetox revisions: - - 83c4b4359ac4 - a177ac3c752c + - 83c4b4359ac4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_fingerprint_similarity owner: recetox revisions: - - fd890f162ce6 - 84af792d3a78 + - fd890f162ce6 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_formatter @@ -111,8 +111,8 @@ tools: - name: matchms_metadata_match owner: recetox revisions: - - 330b0dfae8da - 03bc9b7f40f6 + - 330b0dfae8da tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_metadata_merge @@ -156,8 +156,8 @@ tools: - name: matchms_split owner: recetox revisions: - - 0cf68b536cd1 - ea6c5636c0cf + - 0cf68b536cd1 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: matchms_subsetting @@ -218,8 +218,8 @@ tools: - name: ramclustr_define_experiment owner: recetox revisions: - - 5f2b58dadb39 - f2c1d0bbb074 + - 5f2b58dadb39 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: ramclustr @@ -234,17 +234,17 @@ tools: revisions: - 79ad928a0dae - 7b42ee54d757 - - c53a97599181 - ec196e27a61a + - c53a97599181 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_clusters owner: recetox revisions: - - 149b9cc7499b - - 18ec7635bac6 - f3a18e020cdd - 59c393d35e0e + - 18ec7635bac6 + - 149b9cc7499b tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_compute_template @@ -252,36 +252,36 @@ tools: revisions: - 134be5abb208 - 50b9918aeff2 - - 481d769e2f7a - dfebc82ba1f0 + - 481d769e2f7a tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_correct_time owner: recetox revisions: - - a82db010c53e + - 501a232f3cd5 - 51332c2520c7 - 02c772a49998 - 9064aecc78a7 + - a82db010c53e - 30bf4e35da3e - - 501a232f3cd5 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_generate_feature_table owner: recetox revisions: - - e7305ba0dd38 - - 89178a72388a - b341cfd4baf8 + - 89178a72388a - b3413f335327 + - e7305ba0dd38 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: recetox_aplcms_merge_known_table owner: recetox revisions: - - cf061712a184 - dd7bbc2b99d1 - b7c8a44b9cc1 + - cf061712a184 - 17a48d0a80f4 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -312,8 +312,8 @@ tools: - name: recetox_xmsannotator_advanced owner: recetox revisions: - - 2c6fa447f6a0 - 6b5dec818827 + - 2c6fa447f6a0 tool_panel_section_label: Metabolomics tool_shed_url: toolshed.g2.bx.psu.edu - name: rename_annotated_feature diff --git a/usegalaxy.org.au/metagenomic_analysis.yml b/usegalaxy.org.au/metagenomic_analysis.yml index 9095a339c..95c419fb5 100644 --- a/usegalaxy.org.au/metagenomic_analysis.yml +++ b/usegalaxy.org.au/metagenomic_analysis.yml @@ -17,8 +17,8 @@ tools: - name: cat_summarise owner: iuc revisions: - - a8216def322b - 7f1aaa1932d8 + - a8216def322b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: checkm_analyze @@ -90,20 +90,20 @@ tools: - name: dada2_assigntaxonomyaddspecies owner: iuc revisions: - - 76d3d2b10738 - - 63f86089423e - 65db807336bc - 7c2100246a2f + - 76d3d2b10738 + - 63f86089423e - 5b5a7af9fbb4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_dada owner: iuc revisions: - - 18a502a9d287 - - 00f5005840fa - 96336c6a2bb7 + - 00f5005840fa - 84fd33a60b35 + - 18a502a9d287 - 1c35dadbe76f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -111,39 +111,39 @@ tools: owner: iuc revisions: - addaf9d22850 - - a9f4a217dcd6 - - 34e55239e68b - f732237754fc + - 34e55239e68b - e8fba04706d3 + - a9f4a217dcd6 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_learnerrors owner: iuc revisions: - - 04c15826a0b8 + - 75403243703a - 0776d824d896 - 5fe3edf19b9c + - 04c15826a0b8 - 8c202e741d68 - - 75403243703a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_makesequencetable owner: iuc revisions: - - e96bbb9e24ea - 8470de786d47 - 1c9b3bcd4261 - - 43c99742158b - 75c8945b0da2 + - e96bbb9e24ea + - 43c99742158b tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_mergepairs owner: iuc revisions: - - 84743da21318 - 306a40d4bb8f - - 5c865a382933 + - 84743da21318 - 35176674168c + - 5c865a382933 - 1d75bd0595e2 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu @@ -151,40 +151,40 @@ tools: owner: iuc revisions: - 32c9ea835770 - - 78faebd0879c + - 8daf4564ccda - 555ccac8a4c5 - ac72310b038a - - 8daf4564ccda + - 78faebd0879c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_plotqualityprofile owner: iuc revisions: - - f947b4bb5107 - d60df8727f59 - - cae017b76acb - a58e4a43f49c - 7b8cb2b02978 + - cae017b76acb + - f947b4bb5107 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_removebimeradenovo owner: iuc revisions: - - 04144473e59e + - 073608a50ac3 + - 1bc3657cd694 - 7136e9ab70db + - 04144473e59e - 7f3b59dee073 - - 1bc3657cd694 - - 073608a50ac3 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: dada2_seqcounts owner: iuc revisions: - - d943081510da - 19299bb1c6af + - d943081510da + - a7817705348e - 0a1224c4b781 - 9058d8943303 - - a7817705348e tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: fasttree @@ -197,14 +197,14 @@ tools: - name: gtdbtk_classify_wf owner: iuc revisions: - - a68b985913ab - - f8f56dd6449f - 4d9445dff47b - - c4db8c4de66f - - b907a3c0434f - - 65d52c693b8e - 5c7ba3d85a01 - dbf1798c0dcc + - c4db8c4de66f + - a68b985913ab + - 65d52c693b8e + - f8f56dd6449f + - b907a3c0434f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: hifiasm_meta @@ -231,25 +231,25 @@ tools: - name: humann2_regroup_table owner: iuc revisions: + - e66ab198ec15 - bd7a9c6efb10 - 6aad8ca3918b - - e66ab198ec15 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_renorm_table owner: iuc revisions: + - d77397f09da1 - b084117133af - c6676a890f50 - - d77397f09da1 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2_unpack_pathways owner: iuc revisions: - - cad93abecac9 - 7f208f1eb64f - 9704f1a3b32d + - cad93abecac9 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann2 @@ -267,8 +267,8 @@ tools: - name: humann_barplot owner: iuc revisions: - - 523ae8314ef5 - 5fea25ee6275 + - 523ae8314ef5 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_join_tables @@ -288,33 +288,33 @@ tools: - name: humann_regroup_table owner: iuc revisions: - - 31c6d107e7a5 + - 8237a0f225db - e88b731dad59 + - 31c6d107e7a5 - c409a495841f - 79706f10d680 - - 8237a0f225db tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rename_table owner: iuc revisions: - - 094ad9c068af - - 714d5a28cc5c - 71ea608ddfa3 - - 172920f67a84 - - aabf8cfb8fef - d24841f5c3d2 + - 714d5a28cc5c + - aabf8cfb8fef + - 094ad9c068af + - 172920f67a84 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_renorm_table owner: iuc revisions: - - 12fb63b5f63f + - d7e9a3c41657 + - 4137b492233e - 2bdd84912a2b - a293a742194f - a4d7148ccee4 - - d7e9a3c41657 - - 4137b492233e + - 12fb63b5f63f tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_rna_dna_norm @@ -326,20 +326,20 @@ tools: - name: humann_split_stratified_table owner: iuc revisions: + - 64bc7acc22a9 - 75bedfb2078b - - 6fcb8ac37a3e + - 97f7bb0851e7 - cf87759761eb - - 64bc7acc22a9 - - e2c71b852aba - a92c06a3afa7 - - 97f7bb0851e7 + - 6fcb8ac37a3e + - e2c71b852aba tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_split_table owner: iuc revisions: - - e9d12c223a80 - 81c5dd1c777f + - e9d12c223a80 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann_strain_profiler @@ -351,22 +351,22 @@ tools: - name: humann_unpack_pathways owner: iuc revisions: - - 5e5a999ffaa9 - - 4033827c76b8 + - 2d35528d2141 - 4e5e73d03f0d + - 4033827c76b8 - c82508e76ad1 - - 2d35528d2141 + - 5e5a999ffaa9 - 080ea153677c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: humann owner: iuc revisions: - - 6b7622dda516 - - 95bf7479d53c - - fc6c328c292f - 2cd76b089570 + - fc6c328c292f - c2803012bbb3 + - 6b7622dda516 + - 95bf7479d53c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: itsx @@ -427,8 +427,8 @@ tools: - name: khmer_normalize_by_median owner: iuc revisions: - - 4d23ab83ea29 - b1fe2ef3d244 + - 4d23ab83ea29 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: khmer_partition @@ -447,17 +447,17 @@ tools: - name: kraken2 owner: iuc revisions: + - 4a9da2b6c2e3 - cdee7158adf3 - 20e2f64aa1fe - - 4a9da2b6c2e3 - 328c607150ff tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken2tax owner: devteam revisions: - - 50bd98b3ae5a - f03c7ba8d8bc + - 50bd98b3ae5a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_biom @@ -469,8 +469,8 @@ tools: - name: kraken_filter owner: devteam revisions: - - 67236d921e83 - 5bee9adae474 + - 67236d921e83 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_report @@ -483,8 +483,8 @@ tools: - name: kraken_taxonomy_report owner: iuc revisions: - - 27d65c78863c - bfae8da6082c + - 27d65c78863c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: kraken_translate @@ -496,8 +496,8 @@ tools: - name: kraken owner: devteam revisions: - - 766d5f63b0f4 - 8ba2174315aa + - 766d5f63b0f4 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_alpha_diversity @@ -516,15 +516,15 @@ tools: - name: krakentools_combine_kreports owner: iuc revisions: - - 3d2cffa2c4ab - 073c867c5244 + - 3d2cffa2c4ab tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_extract_kraken_reads owner: iuc revisions: - - f329328da134 - 4bf1e2701504 + - f329328da134 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: krakentools_kreport2krona @@ -538,8 +538,8 @@ tools: - name: krakentools_kreport2mpa owner: iuc revisions: - - d33cf727ed94 - bb96a1e6583d + - d33cf727ed94 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: lotus2 @@ -569,12 +569,12 @@ tools: - name: merge_metaphlan_tables owner: iuc revisions: + - 7f5d7b0e9884 - 0270541aaf46 - - 327d9f4cc95f - 3cc4a60615c0 - - 7f5d7b0e9884 - - 2cff76cf35c6 + - 327d9f4cc95f - e073891b2afc + - 2cff76cf35c6 - 27250f92a01a - 4fd3b5d8706b tool_panel_section_label: Metagenomic Analysis @@ -582,9 +582,9 @@ tools: - name: metabat2 owner: iuc revisions: + - 708abf08a626 - 76bc4efa1aeb - eb50e7eca3dc - - 708abf08a626 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metadegalaxy_pear_stats @@ -650,26 +650,26 @@ tools: - name: metaphlan2krona owner: iuc revisions: - - fdbd63e92b01 - ebb74774457e + - fdbd63e92b01 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metaphlan owner: iuc revisions: - - 740fd2d16a28 - - 289b3807e80c + - fd69c607b43f + - ec368db926f4 - 6dee4abadccb - - 1a037928504c - - a92a632c4d9b - - 1a6cdf55390f - a16313517e55 - - b89b0765695d - - fd69c607b43f - - 2131d7dca455 - ff8f55893e7d - - ec368db926f4 + - 740fd2d16a28 + - 2131d7dca455 + - a92a632c4d9b - ef65b083bd0c + - 1a6cdf55390f + - b89b0765695d + - 1a037928504c + - 289b3807e80c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: metawrapmg_binning @@ -689,6 +689,7 @@ tools: owner: iuc revisions: - 87064cb77a52 + - 40ebae5bbe51 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: phyloseq_ordination_plot @@ -707,15 +708,15 @@ tools: - name: picrust2_hsp owner: iuc revisions: - - 6eafc1e01a8c - 3b133b8d578a + - 6eafc1e01a8c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_metagenome_pipeline owner: iuc revisions: - - 415cb5d91168 - 709adbfcf308 + - 415cb5d91168 tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_pathway_pipeline @@ -728,15 +729,15 @@ tools: - name: picrust2_pipeline owner: iuc revisions: - - d6bb2e3febda - 540aedfc81c7 + - d6bb2e3febda tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_place_seqs owner: iuc revisions: - - 680fb3eb574c - 73b56418e7f4 + - 680fb3eb574c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust2_shuffle_predictions @@ -755,8 +756,8 @@ tools: - name: picrust_compare_biom owner: iuc revisions: - - 0ba7dfaa941d - 8e2ac1b8f70a + - 0ba7dfaa941d tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: picrust_format_tree_and_trait_table @@ -793,34 +794,34 @@ tools: - name: polypolish owner: iuc revisions: - - 915637bd1d1a - f355085dd2aa + - 915637bd1d1a tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: recentrifuge owner: iuc revisions: - - d4fbfd31696c - 591175c0f051 + - d4fbfd31696c tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: staramr owner: nml revisions: - - be818ae858e4 - 2fd4d4c9c5c2 - aeaa20b96ef2 + - be818ae858e4 + - 4b9a8031ab74 - 3b22de20bd4b - - 141afacabcfa - 4d83eccf5f81 - - 4b9a8031ab74 + - 141afacabcfa tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu - name: vsearch owner: iuc revisions: - - 9495df9dd6ef - 576963db5f1b - b3c7199d8786 + - 9495df9dd6ef tool_panel_section_label: Metagenomic Analysis tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/mothur.yml b/usegalaxy.org.au/mothur.yml index 8869ba2d6..350bb5efe 100644 --- a/usegalaxy.org.au/mothur.yml +++ b/usegalaxy.org.au/mothur.yml @@ -80,8 +80,8 @@ tools: - name: mothur_chimera_vsearch owner: iuc revisions: - - 12e856482d26 - bdb4a58a2025 + - 12e856482d26 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_chop_seqs @@ -732,8 +732,8 @@ tools: - name: mothur_summary_single owner: iuc revisions: - - 2344ed181ae6 - 72be09dfd803 + - 2344ed181ae6 tool_panel_section_label: Mothur tool_shed_url: toolshed.g2.bx.psu.edu - name: mothur_summary_tax diff --git a/usegalaxy.org.au/multiple_alignments.yml b/usegalaxy.org.au/multiple_alignments.yml index 7cb3d6291..72466a344 100644 --- a/usegalaxy.org.au/multiple_alignments.yml +++ b/usegalaxy.org.au/multiple_alignments.yml @@ -2,39 +2,39 @@ tools: - name: cactus_cactus owner: galaxy-australia revisions: - - 9422c5a87ee2 - - 8b67dd48fec1 - - 9baa871cb1d1 - - 6ae5a7b5a0a2 + - 9eeb13a92d79 - 2263989660f5 - 098506c54016 - cd07731e4434 - - 80f03df2e2ce - - 9eeb13a92d79 - - bdfbaf0c10aa - 48c13389050d + - 8b67dd48fec1 + - bdfbaf0c10aa - 94b8c6013083 + - 80f03df2e2ce + - 9422c5a87ee2 - a74dbfee5a86 + - 6ae5a7b5a0a2 + - 9baa871cb1d1 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cactus_export owner: galaxy-australia revisions: - 3ff17bad4006 - - '764845535798' - - c18157c68134 - - fc2e49f91e52 - - 4a60927aaca5 - - 5abf2c2249aa - be78f13134e2 - - f14193ec1f50 - - 2e093badc689 + - f0af8936ed41 + - 5abf2c2249aa + - aaa0d6a8b808 - d7ce0ec78e51 + - 4a60927aaca5 - bc3831dd65c1 - - d390fe1567dc - - aaa0d6a8b808 - - f0af8936ed41 - c44f824c051a + - c18157c68134 + - '764845535798' + - f14193ec1f50 + - fc2e49f91e52 + - d390fe1567dc + - 2e093badc689 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: cdhit @@ -46,8 +46,8 @@ tools: - name: chromeister owner: iuc revisions: - - b768cc4cca40 - e483be1014b6 + - b768cc4cca40 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: clustalw @@ -67,61 +67,61 @@ tools: - name: mafft owner: rnateam revisions: - - f0d493f8f84f + - f1a5908ea2cb + - 6f28e90db932 + - bf28a8cff401 + - c5908940967d - a65296ffb4a0 - 15974dd17515 - 8e649f27aa0d - - bf28a8cff401 - - f1a5908ea2cb - - c5908940967d - - 6f28e90db932 + - f0d493f8f84f tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_delta_filter owner: iuc revisions: + - fbca557a4847 - e8fdceffea4c - b3acbb3a6af0 - - fbca557a4847 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_dnadiff owner: iuc revisions: - - c9685bc0407c - - 60698466facd - 5561a1193611 + - 60698466facd + - c9685bc0407c tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummer owner: iuc revisions: - 48823c9635a4 - - bcd65de9725b - 57f042937ba7 + - bcd65de9725b tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_mummerplot owner: iuc revisions: - - ebe3b0f84de9 - - 4fc0cb2ac8ae - fb43e8887350 + - 4fc0cb2ac8ae + - ebe3b0f84de9 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_nucmer owner: iuc revisions: - - 636b049e6141 - 7cd7a55a678d + - 636b049e6141 - e18267f90096 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu - name: mummer_show_coords owner: iuc revisions: - - 959c1f8dae95 - cf3c9489c088 + - 959c1f8dae95 - b4124df98b26 tool_panel_section_label: Multiple Alignments tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/nanopore.yml b/usegalaxy.org.au/nanopore.yml index d9cfc60de..6844fa186 100644 --- a/usegalaxy.org.au/nanopore.yml +++ b/usegalaxy.org.au/nanopore.yml @@ -8,10 +8,10 @@ tools: - name: dorado_pod5_convert owner: galaxy-australia revisions: - - 9aa9d92c3c51 - 18a8d140ec6f - - 28928576e1ea + - 9aa9d92c3c51 - 7c47b3c9e493 + - 28928576e1ea tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: dorado_trimming @@ -23,30 +23,30 @@ tools: - name: dorado owner: galaxy-australia revisions: - - 6942f170cc43 + - 99c9427219d3 - 63d8ecfcfab1 + - 6942f170cc43 - fc5b6491cf78 - - 99c9427219d3 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus_pipeline owner: iuc revisions: - - fc8804320156 - - 72b5e9dda577 + - a7228a7ea146 - 0e9e7fcdd543 + - 72b5e9dda577 - 79e9a869f40e - - a7228a7ea146 - cb34f00cc10f + - fc8804320156 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_consensus owner: iuc revisions: - - d6cddc06aeae - - fa11aa8103b2 - 18505fe2bdb1 + - fa11aa8103b2 - db25ec99c3ea + - d6cddc06aeae tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: medaka_variant_pipeline @@ -58,15 +58,15 @@ tools: - name: medaka_variant owner: iuc revisions: - - 0f5f4a208660 + - 2bf63b38ee9b - 43815fa60f3a - - cc36773a3681 - 19f3b583a9b3 + - edf6d4003fad + - cc36773a3681 + - 0f5f4a208660 - 222669c4afb6 - - eb746fa6f514 - ec699520444c - - 2bf63b38ee9b - - edf6d4003fad + - eb746fa6f514 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanocompore_sampcomp @@ -85,44 +85,44 @@ tools: - name: nanoplot owner: iuc revisions: - - edbb6c5028f5 + - a38bdcec9e4c - a3c4fe6f49ab - - 7b379e98b9a9 + - edbb6c5028f5 - a02b8b3f5a0c - - 0f1c34698076 - - a38bdcec9e4c - 645159bcee2d + - 0f1c34698076 + - 7b379e98b9a9 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_eventalign owner: bgruening revisions: - - 3b6f94fc7e1d - 85a394edc247 + - 3b6f94fc7e1d - d219b6d8158a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_methylation owner: bgruening revisions: - - a8d4be409446 - 90a922f32523 - be95355fef8d + - a8d4be409446 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_polya owner: bgruening revisions: - - 449e9aeded2d - 4857d5bcce52 + - 449e9aeded2d - d376944466bf tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: nanopolish_variants owner: bgruening revisions: - - de5b3d8f5b90 - a3afc5f0a96c + - de5b3d8f5b90 - bec636361cfd tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu @@ -130,8 +130,8 @@ tools: owner: iuc revisions: - 93d623d9979c - - 543cbeef3949 - 5f76b20953e5 + - 543cbeef3949 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_events @@ -150,8 +150,8 @@ tools: - name: poretools_hist owner: iuc revisions: - - d1805f9c4c82 - 47936349f3e9 + - d1805f9c4c82 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_nucdist @@ -176,15 +176,15 @@ tools: - name: poretools_qualpos owner: iuc revisions: - - 2e22ebec211a - 626b6c2be5c2 + - 2e22ebec211a tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_squiggle owner: iuc revisions: - - ce8af9373061 - 26e6c9362b7b + - ce8af9373061 tool_panel_section_label: Nanopore tool_shed_url: toolshed.g2.bx.psu.edu - name: poretools_stats diff --git a/usegalaxy.org.au/none.yml b/usegalaxy.org.au/none.yml index 248a14891..dd68353f0 100644 --- a/usegalaxy.org.au/none.yml +++ b/usegalaxy.org.au/none.yml @@ -2,8 +2,8 @@ tools: - name: amrfinderplus_data_manager_build owner: iuc revisions: - - a5921c09b7b7 - 592ef3959907 + - a5921c09b7b7 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: blast_datatypes @@ -27,19 +27,19 @@ tools: - name: data_manager_bakta owner: iuc revisions: + - baceff842902 + - adfd6bf710bd + - 97b1b5ad1cda - d74850cf4e42 - 3e73c97f025d - - 97b1b5ad1cda - - adfd6bf710bd - - baceff842902 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam revisions: - 1586b111d2a3 - - 9dd107db92c2 - 83da94c0e4a6 + - 9dd107db92c2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_build_bracken_database @@ -51,13 +51,13 @@ tools: - name: data_manager_build_kraken2_database owner: iuc revisions: - - 2f27f3b86827 - - 19b6a2f0dbe2 - - ed1518ce2237 - - 13851aefa67a - 1e34d2e3d285 - - e9ee4d074d5d + - ed1518ce2237 - e4b4837f06f5 + - e9ee4d074d5d + - 2f27f3b86827 + - 13851aefa67a + - 19b6a2f0dbe2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder @@ -76,30 +76,30 @@ tools: - name: data_manager_cat owner: iuc revisions: - - 74af283d8ebd - 472dabcb03bf + - 74af283d8ebd tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_dada2 owner: iuc revisions: + - 48a42ca61006 - 38ccd4589990 - 5711fc06a63e - - 48a42ca61006 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_diamond_database_builder owner: bgruening revisions: - - 5a0d0bee4f8d - 4a08b7b76b78 + - 5a0d0bee4f8d tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_eggnog_mapper_abspath owner: galaxyp revisions: - - 81a286e4c5a2 - fcb8bdd124f4 + - 81a286e4c5a2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_fetch_busco @@ -125,16 +125,16 @@ tools: - name: data_manager_gatk_picard_index_builder owner: devteam revisions: - - 9a40272f56d0 - 6287d0ee459e + - 9a40272f56d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_gemini_database_downloader owner: iuc revisions: - - 27a6a256cd23 - 52b6a4d98009 - b4b2b284230a + - 27a6a256cd23 - 172815da3d41 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,9 +160,9 @@ tools: - name: data_manager_humann_database_downloader owner: iuc revisions: - - 87febc68b45b - - fea85c467896 - 19bbd19b74b3 + - fea85c467896 + - 87febc68b45b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_interproscan @@ -175,8 +175,8 @@ tools: - name: data_manager_kallisto_index_builder owner: iuc revisions: - - 15c2fc266540 - 4c7ebbad42cf + - 15c2fc266540 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mash_sketch_builder @@ -194,12 +194,12 @@ tools: - name: data_manager_metaphlan_database_downloader owner: iuc revisions: - - d8dc037e3c13 - 4ba60cb14cb0 - - 9c43baa60906 - - 0cb27ea69dc1 + - d8dc037e3c13 - 2c61c30a57e7 + - 9c43baa60906 - 5fe20c915fa6 + - 0cb27ea69dc1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_mitos @@ -212,18 +212,18 @@ tools: - name: data_manager_mothur_toolsuite owner: iuc revisions: - - 0db22932bc39 - - aec831b54a5b - 9d09724f2bf1 + - aec831b54a5b + - 0db22932bc39 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pangolearn owner: iuc revisions: - - df30a2f1db55 - - ed7a967cb11b - 29c738066906 + - df30a2f1db55 - 6e24e79d3d69 + - ed7a967cb11b tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_pharokka @@ -241,8 +241,8 @@ tools: - name: data_manager_sam_fasta_index_builder owner: devteam revisions: - - ad90c2da4f38 - 3e4d45aca422 + - ad90c2da4f38 - 1865e693d8b2 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu @@ -262,17 +262,17 @@ tools: - name: data_manager_star_index_builder owner: iuc revisions: - - 64deddb6a8ec - - c520a52b5174 - d63c1442407f + - c520a52b5174 + - 64deddb6a8ec tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_twobit_builder owner: devteam revisions: + - 9946bc39c834 - 625fd9476402 - 94a50db37d1a - - 9946bc39c834 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: data_manager_vep_cache_downloader @@ -326,8 +326,8 @@ tools: - name: overlay_segmentation_mask owner: imgteam revisions: - - 22e573b7dcb1 - 8ad39f493587 + - 22e573b7dcb1 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: package_atlas_3_10 @@ -783,8 +783,8 @@ tools: - name: rdata_xcms_datatypes owner: lecorguille revisions: - - 544f6d2329ac - d64562a4ebb3 + - 544f6d2329ac tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: rsem_datatypes @@ -796,11 +796,11 @@ tools: - name: salsa owner: iuc revisions: - - 58a870ef434c - - 9a22227bb6d0 - - ba7b0f11e470 - f77f7a7f3b83 + - ba7b0f11e470 + - 58a870ef434c - ab5b7f6b7198 + - 9a22227bb6d0 tool_panel_section_label: None tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_ampliconclip diff --git a/usegalaxy.org.au/phylogenetics.yml b/usegalaxy.org.au/phylogenetics.yml index 7a596d2fd..e9a260da0 100644 --- a/usegalaxy.org.au/phylogenetics.yml +++ b/usegalaxy.org.au/phylogenetics.yml @@ -20,8 +20,8 @@ tools: - name: gubbins owner: iuc revisions: - - 637ec5d5368c - 96e6283e4745 + - 637ec5d5368c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hybpiper @@ -33,66 +33,66 @@ tools: - name: hyphy_absrel owner: iuc revisions: - - 107d3ba7024a - - 5a7c56a5cc08 + - '841557158611' + - 8834daeb9892 + - 3f59ebfbfe3d - 6a457678efcb - - c78f3d7dd1db + - 81e66674859e - 26de3a7b1cb9 - - 3f59ebfbfe3d - - d7c7ef3353fe - - f04a1264e2a2 - - f73435dc282b - - 8834daeb9892 - b89cac5156ec + - c78f3d7dd1db + - 3b8b5bde0bd9 + - f73435dc282b + - 107d3ba7024a + - 5a7c56a5cc08 + - f04a1264e2a2 + - d033ffc1c161 - cce7b18495e4 - - 81e66674859e + - d7c7ef3353fe - a6619171428e - - '841557158611' - - d033ffc1c161 - - 3b8b5bde0bd9 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: hyphy_gard owner: iuc revisions: + - 6223845127ea + - 4755f52427c4 + - df47d4845b62 - 3b96e92e8ec3 + - 88c4aa435ded + - b0af57c1a968 - 7a2092844346 - - 4755f52427c4 - - aa8cc71438cf - - 5b777002c2de - - 659517798cc4 - - 6283babe736e - e75442c7f4da - - 02b8758214b0 - - df47d4845b62 - - 6223845127ea + - 6283babe736e + - 659517798cc4 + - 6a726db04d4b - 5fcd1ece3a6e - - 88c4aa435ded - a185b079b095 - - 6a726db04d4b - - b0af57c1a968 + - 02b8758214b0 + - aa8cc71438cf + - 5b777002c2de tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: iqtree owner: iuc revisions: - - f97743d52b87 + - 70acec670c30 - f87ac61981f0 - - c1d53e95327f - - 24d024316465 - b8476e82ac20 - - 111bd54f6bc4 - - 70acec670c30 + - c1d53e95327f - d1c340a5664b + - 111bd54f6bc4 + - f97743d52b87 + - 24d024316465 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: nextclade owner: iuc revisions: - - feb40665d7cd - - 9e10ba792be2 - 4f6349228462 + - feb40665d7cd - daddf188c13f + - 9e10ba792be2 tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: orthofinder_onlygroups @@ -105,25 +105,25 @@ tools: owner: iuc revisions: - 2fa9d4f1b48f - - abf6dbe8c9d7 - - 3a43c3982401 + - ca0d8cf80567 - 437e28791761 - - 81804a978fc0 - - 36912871ccdc - - 2f1019071464 + - 83a69484cb87 + - 3a43c3982401 + - 8ad84c5753ea + - ca337cce3888 - 7bb8726be37c - - ca0d8cf80567 - 14ae456b8cc5 + - b6abccb1f25b - 42a174224817 + - 2f1019071464 + - 5f8727ff21e7 - b7e297c2ede6 - - 9d61d3fa046c - a2099fb98cdb - - ca337cce3888 - - 83a69484cb87 - - b6abccb1f25b - - 8ad84c5753ea - - 5f8727ff21e7 + - 9d61d3fa046c - 03ed9524dcd1 + - abf6dbe8c9d7 + - 81804a978fc0 + - 36912871ccdc tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: phyml @@ -142,23 +142,23 @@ tools: - name: raxml owner: iuc revisions: - - b1e68bbe4cef - - a4b71be30c3c - - 73a469f7dc96 - ea30d3089354 + - b1e68bbe4cef - 29ff6a849eac - ba29b5e2a4be + - 73a469f7dc96 + - a4b71be30c3c tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu - name: roary owner: iuc revisions: - - 91887494eb97 - - 9b2b122d0415 - - 809e42326fc2 - f1ccc8a6eb05 - dbe2b2204555 - - e88a7de55d6e + - 809e42326fc2 + - 9b2b122d0415 - 15ac71df11a0 + - 91887494eb97 + - e88a7de55d6e tool_panel_section_label: Phylogenetics tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/picard.yml b/usegalaxy.org.au/picard.yml index 1483f4cec..beb608e1c 100644 --- a/usegalaxy.org.au/picard.yml +++ b/usegalaxy.org.au/picard.yml @@ -2,14 +2,14 @@ tools: - name: picard owner: devteam revisions: - - 1aac2a13842a - - f6ced08779c4 + - f9242e01365a - fc288950c3b7 - 881d7645d1bf - - 3f254c5ced1d + - f6ced08779c4 - a1f0b3f4b781 - b502c227b5e6 + - 3f254c5ced1d - 7d34178f2812 - - f9242e01365a + - 1aac2a13842a tool_panel_section_label: Picard tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomic_ai.yml b/usegalaxy.org.au/proteomic_ai.yml index 5714dac72..b17531596 100644 --- a/usegalaxy.org.au/proteomic_ai.yml +++ b/usegalaxy.org.au/proteomic_ai.yml @@ -3,17 +3,17 @@ tools: owner: galaxy-australia revisions: - 2f7702fd0a4c - - d00e15139065 + - 6ab1a261520a + - eb085b3dbaf8 + - a58f7eb0df2c + - ca90d17ff51b - e7f1b552a695 + - d00e15139065 + - 3bd420ec162d + - c0e71cb2bd1b - 7fbec959cf2b - 5b85006245f3 - 3f188450ca4f - - c0e71cb2bd1b - - eb085b3dbaf8 - e4a053d67e24 - - ca90d17ff51b - - 3bd420ec162d - - 6ab1a261520a - - a58f7eb0df2c tool_panel_section_label: Proteomic AI tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/proteomics.yml b/usegalaxy.org.au/proteomics.yml index 96f93c12a..74ab74de4 100644 --- a/usegalaxy.org.au/proteomics.yml +++ b/usegalaxy.org.au/proteomics.yml @@ -2,33 +2,33 @@ tools: - name: cardinal_classification owner: galaxyp revisions: + - 277dc652246e + - 4c177985028a - b18329a8ac14 + - 0a18ac48ac53 - b574b84afc4d - f28ad96b76dc - - 277dc652246e - - 0a18ac48ac53 - ece627528a78 - - 4c177985028a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_combine owner: galaxyp revisions: - - b41107d8fe89 - - a9a28e46d54a - - e988563cc6e5 - - e215f71d7983 - bf06d196e23d - 525f201b86c1 + - e215f71d7983 + - e988563cc6e5 + - b41107d8fe89 + - a9a28e46d54a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_data_exporter owner: galaxyp revisions: - 56da27be956a - - bb6397b94018 - 8da3511c9467 - 4fbffddde8cd + - bb6397b94018 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_filtering @@ -36,47 +36,47 @@ tools: revisions: - b8c79e70516d - 528fb09022be - - a8157342d9a3 - 890845926d4b - f23d67e28cc8 + - a8157342d9a3 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_mz_images owner: galaxyp revisions: - - a69865da6f80 + - a95a82eb4d50 + - ae304a72db7b - 80600735685d + - a69865da6f80 - 59e85306eae5 - 25b83cbd596a - - ae304a72db7b - - a95a82eb4d50 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_preprocessing owner: galaxyp revisions: - - 611d80c0e29d + - 798da6bdff3d - e0669b1854b1 - f1897eb07081 + - 611d80c0e29d - ed9ed1e6cca2 - 83aac7741200 - - 798da6bdff3d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_quality_report owner: galaxyp revisions: - - a7fb9b395ddf - - 74b61bf5bc4b - d426a9107a6c - 5a35e3a8d013 + - a7fb9b395ddf + - 74b61bf5bc4b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: cardinal_segmentations owner: galaxyp revisions: - - 82f6c2f4332d - cc430977c8ff + - 82f6c2f4332d - df2187f9013b - 91f0f5922011 tool_panel_section_label: Proteomics @@ -84,11 +84,11 @@ tools: - name: cardinal_spectra_plots owner: galaxyp revisions: - - 10566783d718 - - ba92b59cd529 - - 1693b2126f30 - d2483487e077 - c5aa9fca18c6 + - 10566783d718 + - 1693b2126f30 + - ba92b59cd529 - 043f9c91f686 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -107,10 +107,10 @@ tools: - name: diann owner: galaxyp revisions: + - ae4dc0c041f9 - bf0728e000cd - - 9fa3dbf06f17 - ff8c9e0e8a7b - - ae4dc0c041f9 + - 9fa3dbf06f17 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: diapysef @@ -123,31 +123,31 @@ tools: owner: galaxyp revisions: - d263296cd73e - - eac99effe86f - d0ea7589e95f + - eac99effe86f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_quantify owner: galaxyp revisions: - - 1c5cbf8f79ce - - 4081e4faa4ab - 0fa397f4f40b + - 4081e4faa4ab + - 1c5cbf8f79ce tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_searchtolib owner: galaxyp revisions: - - fb192dd6658a - 36880dfd9fa7 + - fb192dd6658a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: encyclopedia_walnut owner: galaxyp revisions: - - ce1a157a41bd - - d6a4dfdad269 - 0d2e93e01e68 + - d6a4dfdad269 + - ce1a157a41bd tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: flashlfq @@ -159,38 +159,38 @@ tools: - name: maldi_quant_peak_detection owner: galaxyp revisions: + - e66f552a3c47 - d286ff4600dd - 160538a890a6 - - e66f552a3c47 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maldi_quant_preprocessing owner: galaxyp revisions: - - 71411ac28268 - 60ee8c592b13 + - 71411ac28268 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant_mqpar owner: galaxyp revisions: - - 9cb7dcc07dae - 3fc2116ac6d9 + - 9cb7dcc07dae tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: maxquant owner: galaxyp revisions: - - 4d17fcdeb8ff - - 9c52362ae7bb - - 2133b0be850a - - 1f39c833f65f - - 7f432d87c82c + - 97a7f34fcb6a - f522c08e900c + - 9c52362ae7bb - e42225f8a659 - - 97a7f34fcb6a - 37d669de2828 + - 4d17fcdeb8ff + - 1f39c833f65f - 837224ad1694 + - 7f432d87c82c + - 2133b0be850a tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metanovo @@ -203,8 +203,8 @@ tools: owner: galaxyp revisions: - e63db1aa82ee - - 85b8866f06d7 - a72ac2c7cc5b + - 85b8866f06d7 - 0ed07016d668 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -212,17 +212,17 @@ tools: owner: galaxyp revisions: - 1974224d63c2 - - 352b37c66d97 - 767c1d761aaf - 990b4560ead7 + - 352b37c66d97 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_filter owner: galaxyp revisions: - - deaf035bbe9f - 4f359549383c - 35cc7ca0bdc7 + - deaf035bbe9f - 99450519d727 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -230,17 +230,17 @@ tools: owner: galaxyp revisions: - 06f6826d380c + - e79958768a2c - c1343e3389ca - c7745841de24 - - e79958768a2c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: metaquantome_stat owner: galaxyp revisions: - - da986f83631b - b9d453dca8d3 - d2eac53666f0 + - da986f83631b - d46d64e7964d tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -249,15 +249,15 @@ tools: revisions: - 9bf325045235 - 8bd7734309f6 - - 1199751329b0 - 944b43462104 + - 1199751329b0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: morpheus owner: galaxyp revisions: - - 8295d959ca28 - e0104a9f20f0 + - 8295d959ca28 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: msconvert @@ -287,53 +287,53 @@ tools: owner: galaxyp revisions: - f4be248c3d47 - - 01dbaf6a57e0 - - 8960fb791701 - 4e77b8f12cd3 + - 8960fb791701 + - 01dbaf6a57e0 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_decoydatabase owner: galaxyp revisions: - - 25529df60a81 - 370141bc0da3 - 06cca574e337 + - 25529df60a81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_falsediscoveryrate owner: galaxyp revisions: - - 9cdf15d3cfc8 - - c9eff69a7c62 - f7fef900f5b2 - - 6ccbf9a2072c + - 9cdf15d3cfc8 - 518b1730cf2a + - 6ccbf9a2072c + - c9eff69a7c62 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_featurefindermultiplex owner: galaxyp revisions: - - ca88bd28f116 - dff6c756eee5 - - 5e948629bc73 + - ca88bd28f116 - 9876bda3ec53 + - 5e948629bc73 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fidoadapter owner: galaxyp revisions: + - 1595601708ec + - 41859bbdc16e - 890025d6e426 - 658494a2cb00 - - 41859bbdc16e - - 1595601708ec tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileconverter owner: galaxyp revisions: + - 2a93a25f0599 - 9b7977080f6d - 5ad0b5bf1deb - - 2a93a25f0599 - 6634cad7d797 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu @@ -342,115 +342,115 @@ tools: revisions: - fe4e4587d265 - 05d5e1ddc985 - - 0bb5056cb775 - d6878d27f051 + - 0bb5056cb775 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_fileinfo owner: galaxyp revisions: - - 5ad830edc021 - 52ba9695e752 - 4af67edd5aef + - 5ad830edc021 - febd569ad26f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_filemerger owner: galaxyp revisions: - - 39e8fde08881 - - 27cba4c5fc42 - - 92352a475eed - b2fc8da99bcc + - 92352a475eed + - 27cba4c5fc42 + - 39e8fde08881 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_highresprecursormasscorrector owner: galaxyp revisions: + - 0efbc235f314 - 9e26f5c770f8 - d413dc49d650 - d3546bb9fd8e - - 0efbc235f314 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idconflictresolver owner: galaxyp revisions: - - ca1740533b59 - - c28f13cab67a - - 3720e349ba2a - 8a04ed1c1d1b + - 3720e349ba2a + - c28f13cab67a + - ca1740533b59 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idfilter owner: galaxyp revisions: - - a5d785af0ad8 - - c55dddc5844a - - 382cde407f81 - c427a8628cbe + - c55dddc5844a - ca799a7246e7 + - a5d785af0ad8 + - 382cde407f81 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmapper owner: galaxyp revisions: - - 8ddb7bab1138 - - adca857b4884 - b5d0905419da - 39caaa778d2e + - 8ddb7bab1138 + - adca857b4884 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_idmerger owner: galaxyp revisions: - 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name: openms_mztabexporter owner: galaxyp revisions: - - 8098330f6d91 - ee860980edc6 + - 8098330f6d91 - 2735db4dd8d9 - bf32e0bcf554 tool_panel_section_label: Proteomics @@ -458,92 +458,92 @@ tools: - name: openms_openswathanalyzer owner: galaxyp revisions: + - 08488066d588 - a2a6e9551046 - 0ced5bc9f4dd - - 08488066d588 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathassaygenerator owner: galaxyp revisions: - de7a553552a6 - - 8c01da82292c - 2a9ff56cb279 + - 8c01da82292c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathconfidencescoring owner: galaxyp revisions: - 1bf940c18d93 - - e8f64a7dc470 - c1809c05ae8c + - e8f64a7dc470 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdecoygenerator owner: galaxyp revisions: + - 9f505cd4428f - f861ec9fbe59 - 496cf619e311 - - 9f505cd4428f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathdiaprescoring owner: galaxyp revisions: + - c99d5004b74f - 0bddef8d144e - d4396637b9f5 - - c99d5004b74f tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathfilesplitter owner: galaxyp revisions: - - 89254095cbf6 - 4bb198c0bd3e - 8b814eafce2c + - 89254095cbf6 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathmzmlfilecacher owner: galaxyp revisions: + - f82b320ceb90 - f9ed7e074900 - 05ec9fb05ed1 - - f82b320ceb90 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathrtnormalizer owner: galaxyp revisions: - - 6e8cc5ed2a9b - - 18826fb8e5db - d31426ef20f6 + - 18826fb8e5db + - 6e8cc5ed2a9b tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_openswathworkflow owner: galaxyp revisions: - - 4a7b96835140 - - 2aebe58de46e - bc63b4d12779 + - 2aebe58de46e + - 4a7b96835140 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peakpickerhires owner: galaxyp revisions: - - 5ae104d0da6e - - 6b01678ec2fc - decc397c3b7e + - 6b01678ec2fc - 3d8d4ada5405 + - 5ae104d0da6e tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_peptideindexer owner: galaxyp revisions: - - e039cc5c7aed - - 5182338d5e7c + - 539a3a4dcc9e - dd173849c3d8 + - 5182338d5e7c - d6aca689dd48 - - 539a3a4dcc9e + - e039cc5c7aed tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_proteinquantifier @@ -565,17 +565,17 @@ tools: - name: openms_textexporter owner: galaxyp revisions: - - 1b03536aa3c9 - d063e2fe4ba4 - 9020199dba0a + - 1b03536aa3c9 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xmlvalidator owner: galaxyp revisions: - - 78c080d36945 - ad2ba3a95a02 - f036e8cf1a55 + - 78c080d36945 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: openms_xtandemadapter @@ -590,8 +590,8 @@ tools: - name: pep_pointer owner: galaxyp revisions: - - 073a2965e3b2 - a6282baa8c6f + - 073a2965e3b2 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: pepquery2 @@ -603,21 +603,21 @@ tools: - name: peptide_genomic_coordinate owner: galaxyp revisions: - - cb0378d2d487 - 5f49ffce52cb + - cb0378d2d487 tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: peptideshaker owner: galaxyp revisions: - - 3634c90301af - - 3ec27b4cee7c - - da885ca16cb2 - 1beff3ddce58 - - 943a34df6047 - a72c48001f7c - - 07ff622ec007 - 7fdd9119cc4f + - 07ff622ec007 + - 943a34df6047 + - 3634c90301af + - da885ca16cb2 + - 3ec27b4cee7c tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: percolator @@ -678,9 +678,9 @@ tools: owner: galaxyp revisions: - 12692567c7f9 - - 1a5690a5eedc - 265c35540faa - a371252a2cf6 + - 1a5690a5eedc tool_panel_section_label: Proteomics tool_shed_url: toolshed.g2.bx.psu.edu - name: validate_fasta_database diff --git a/usegalaxy.org.au/rad_seq.yml b/usegalaxy.org.au/rad_seq.yml index 18a3837d6..35daee129 100644 --- a/usegalaxy.org.au/rad_seq.yml +++ b/usegalaxy.org.au/rad_seq.yml @@ -3,20 +3,20 @@ tools: owner: iuc revisions: - 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- 43e3eeb2e0ec + - c287418eb288 + - 17d39bf0a63a - 97575d01f06b - c5d7050e4ad7 + - 43e3eeb2e0ec - 4e280b27a831 - - c287418eb288 - - 17d39bf0a63a tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_sstacks owner: iuc revisions: - - 0b8c84a7fdb5 - - a819ec3b362d + - cd034465d4a4 - 9586f08634c0 - d9bf483266a1 - - cd034465d4a4 + - a819ec3b362d + - 0b8c84a7fdb5 - 09b8edb56d80 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_tsv2bam owner: iuc revisions: - - 95351dd0fd3f - a4b4bd84f69e - - a9c34a289493 - - bf0e43ab0416 + - 95351dd0fd3f - 69842dd5aa48 + - bf0e43ab0416 - 2645575d1bf2 + - a9c34a289493 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks2_ustacks owner: iuc revisions: - - d1fda11e602f - - cfb504394ae1 - bb0475c884ff - - 912f904a6e1e - d033e1ccb386 + - cfb504394ae1 + - 912f904a6e1e - 8a35a3bc6752 + - d1fda11e602f tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stacks_assembleperead @@ -163,8 +163,8 @@ tools: - name: stacks_populations owner: iuc revisions: - - 95286af4139b - d1fad35bdb4a + - 95286af4139b - d504d945a655 tool_panel_section_label: RAD-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rna_seq.yml b/usegalaxy.org.au/rna_seq.yml index 25c5bd71a..2a0c2c69f 100644 --- a/usegalaxy.org.au/rna_seq.yml +++ b/usegalaxy.org.au/rna_seq.yml @@ -3,18 +3,18 @@ tools: owner: iuc revisions: - 2d4e3aff9dc7 - - 31f8063eedea - cf01dd6c6b1f - 7acb00fc980a + - 31f8063eedea tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba_get_filters owner: iuc revisions: - - 125d20cb23d7 - - 703a2cb3fb38 - 32e542c2a773 + - 125d20cb23d7 - 7a5a2d28c539 + - 703a2cb3fb38 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: arriba @@ -34,8 +34,8 @@ tools: - name: blockclust owner: rnateam revisions: - - dbb6ee3179bc - aab6cf87b40a + - dbb6ee3179bc tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cemitool @@ -90,41 +90,41 @@ tools: owner: devteam revisions: - f648e5180e40 - - e66b9b5b8580 - ad5d061fbdf2 + - e66b9b5b8580 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cufflinks owner: devteam revisions: - - 6926716bbfb5 - e04dbae2abe0 + - 6926716bbfb5 - d080005cffe1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffmerge owner: devteam revisions: - - 86285ddd4512 - - cf747d1bd79a + - 04adc9db1581 - 6a6717a5f421 - 22cf48ad7b16 - - 04adc9db1581 + - 86285ddd4512 + - cf747d1bd79a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffnorm owner: devteam revisions: + - 28b94cfbfdb9 - 6cbfede05833 - 9a854107dbb2 - - 28b94cfbfdb9 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cuffquant owner: devteam revisions: - - 679d93c99757 - 93148c05136f + - 679d93c99757 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: cummerbund @@ -143,55 +143,55 @@ tools: owner: iuc revisions: - 0693ccd171c4 + - 3b36efd62b3e - 8f0181aacb7a - e3b16fd7dd08 - - 3b36efd62b3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: deseq2 owner: iuc revisions: - - 9a882d108833 + - d027d1f4984e - 0696db066a5b - 6a3a025714d3 - - d027d1f4984e + - cd9874cb9019 - 8fe98f7094de + - 9a882d108833 - 24a09ca67621 - - cd9874cb9019 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: dexseq owner: iuc revisions: - 2872c633f07e - - 9a7c5b6d8f1e - 62adf13b86ea - df929f257179 - b47c006d90c5 + - 9a7c5b6d8f1e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: edger owner: iuc revisions: - - 6e53e565fc6a - - 5bf899c13979 - - 0cb907a2a810 + - 070900306913 + - 3d89af8a44f0 - 555659de7321 - - a8305cf0c951 - - 334ce9b1bac5 - ae2aad0a6d50 - - 070900306913 - - f2843df56434 - - 9bdff28ae1b1 + - 334ce9b1bac5 - df0c8d0a5992 - - 3d89af8a44f0 + - a8305cf0c951 + - 9bdff28ae1b1 + - f2843df56434 + - 5bf899c13979 + - 0cb907a2a810 + - 6e53e565fc6a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: egsea owner: iuc revisions: - - fba1660fb717 - 31ea4992b948 + - fba1660fb717 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: express @@ -203,18 +203,18 @@ tools: - name: featurecounts owner: iuc revisions: - - 90d16db017d7 + - af814359d244 + - a37612abf7f9 + - f3a5f075498f + - 7db9d3ea71c9 + - e6a2a912677a - f9d49f5cb597 - - a56fbe2d6ba7 - - 38b6d12edc68 - - 1b851f87fbe0 - 6f66ae7c5f7a + - 1b851f87fbe0 + - 38b6d12edc68 + - a56fbe2d6ba7 - ea04b737afa0 - - f3a5f075498f - - a37612abf7f9 - - af814359d244 - - e6a2a912677a - - 7db9d3ea71c9 + - 90d16db017d7 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: feelnc @@ -238,9 +238,9 @@ tools: - name: gffcompare owner: iuc revisions: + - 0f710191a66d - 3c5e024a18cf - 3c97c841a443 - - 0f710191a66d tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: heinz @@ -252,21 +252,21 @@ tools: - name: hisat2 owner: iuc revisions: + - 6c19daec423d + - a86e80d3c09c - 26371a1df031 - - d4b55e2beb12 - 3fb01a8c902d - - 6c19daec423d - f4af63aaf57a - - a86e80d3c09c - 6ab42baa56e9 + - d4b55e2beb12 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: htseq_count owner: lparsons revisions: - - 4418229c501e - 916cb26bd9d3 - 67b0b160903a + - 4418229c501e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: isoformswitchanalyzer @@ -279,32 +279,32 @@ tools: owner: iuc revisions: - 87c11c05d238 - - 01247aaf0a10 - - ce5d418183c5 - 5ae5c312d718 + - 01247aaf0a10 - 1c75aa5de15e + - ce5d418183c5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: kallisto_quant owner: iuc revisions: - - c971db6f0fe5 - 10c98fab6c5a - 4f9c4e6566e5 + - c971db6f0fe5 - 40985510cd98 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: limma_voom owner: iuc revisions: - - 119b069fc845 - 708348a17fa1 - 0921444c832d - - d6f5fa4ee473 - e827f9aae031 - 32511f586472 - - 97e06a4c7c75 - 58c35179ebf0 + - d6f5fa4ee473 + - 97e06a4c7c75 + - 119b069fc845 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mircounts @@ -316,8 +316,8 @@ tools: - name: mirdeep2_mapper owner: rnateam revisions: - - a8d24f4b6d95 - dbbe92348c7a + - a8d24f4b6d95 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: mirdeep2_quantifier @@ -360,21 +360,21 @@ tools: - name: rgrnastar owner: iuc revisions: - - 4074fc1940e2 - - b0f2be869d6d - - 980d2a2e1180 - - b9e04854e2bb + - 99b17b74a8cd - 3ea5a2a63fa2 - - c772497b2c32 - e132e7d02a3e - - 5ec75f5dae3c + - 7ed2edc1337f - 4df95e2d7f61 - - 99b17b74a8cd - c7c55b694974 - - 7ed2edc1337f - - 0a563fd2f22e + - c772497b2c32 + - 4074fc1940e2 + - b0f2be869d6d - 79de45b5069b + - 980d2a2e1180 + - b9e04854e2bb - 4014de1b6daf + - 5ec75f5dae3c + - 0a563fd2f22e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: sailfish @@ -386,36 +386,36 @@ tools: - name: salmon owner: bgruening revisions: + - 2c0ca397d302 + - 15cd64d7c58b + - ebab418107f5 - f4d5237a84f6 - 49121db48873 - 53e9709776a0 - - ebab418107f5 - - e3d32471da11 - cc05793bb896 - - 15cd64d7c58b - - 2c0ca397d302 + - e3d32471da11 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: seurat owner: iuc revisions: - fab6ff46e019 - - c0fd285eb553 - - 56242ff81c84 - 8c28affc7c48 + - 56242ff81c84 + - c0fd285eb553 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: stringtie owner: iuc revisions: - - dd4df992d93d - 258d696dbd7e - - 914cfcba0ec8 + - dd4df992d93d - cbf488da3b2c - - cef79931dda5 + - 914cfcba0ec8 + - 1ebd14235b92 - ae618321f34a - 76d290331481 - - 1ebd14235b92 + - cef79931dda5 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: targetfinder @@ -445,55 +445,55 @@ tools: - name: transdecoder owner: iuc revisions: + - 0db979fead3a + - d0d4cef4f967 - ffd1300599a1 - c6334cb383ff - - d0d4cef4f967 - - 0db979fead3a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_abundance_estimates_to_matrix owner: iuc revisions: - d6a479fd4281 - - 74217fbfba4d - ba3720d7e68b + - 74217fbfba4d - bcc5f03f1900 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_align_and_estimate_abundance owner: iuc revisions: + - c2b82a94493e - 2fb4ee002432 - - 478f36effca1 - 56162e446004 - - c2b82a94493e + - 478f36effca1 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_analyze_diff_expr owner: iuc revisions: + - 3f4094b6a565 - fab23c3b5258 - 9ff3765e7172 - - 3f4094b6a565 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_contig_exn50_statistic owner: iuc revisions: - 870ac06dff8e - - 34a018cbee9c - - be3f26533209 - 4687ecf0eb2d + - be3f26533209 + - 34a018cbee9c tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_define_clusters_by_cutting_tree owner: iuc revisions: - 65e7dea767ea - - 5192f657f305 - 33406f5a445c - - c5fbddcac63a - 05ab8d5e04a2 + - 5192f657f305 + - c5fbddcac63a tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_filter_low_expr_transcripts @@ -508,8 +508,8 @@ tools: - name: trinity_gene_to_trans_map owner: iuc revisions: - - 37a1129c89d2 - 964b7efe2639 + - 37a1129c89d2 - c2c039e421af - 7c7fbf13aadd tool_panel_section_label: RNA-seq @@ -517,19 +517,19 @@ tools: - name: trinity_run_de_analysis owner: iuc revisions: + - 1d689e4e1caf - 047c22569787 - 24e94d84adc9 - - 1d689e4e1caf - eafea3083352 tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_samples_qccheck owner: iuc revisions: - - 1812dbc5bb7b - 3a4ac03d1266 - - 9871104ea630 - 04bb8bb7c198 + - 9871104ea630 + - 1812dbc5bb7b tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu - name: trinity_stats @@ -547,14 +547,14 @@ tools: - name: trinity owner: iuc revisions: + - d84caa5a98ad + - cee61b3fcf78 + - 9fa24d5aac68 - 48636f857c4b - 32b86cd8eb50 - - 9fa24d5aac68 - - d84caa5a98ad + - c9cfec002f71 - 8f1c3df4dd49 - d2bc35f3d1c5 - - cee61b3fcf78 - - c9cfec002f71 - db1f362cca3e tool_panel_section_label: RNA-seq tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/rseqc.yml b/usegalaxy.org.au/rseqc.yml index ee524b79e..53b800e78 100644 --- a/usegalaxy.org.au/rseqc.yml +++ b/usegalaxy.org.au/rseqc.yml @@ -2,9 +2,9 @@ tools: - name: rseqc owner: nilesh revisions: - - 080fd5739bb4 + - 473382134e56 - 27e16a30667a - 1a052c827e88 - - 473382134e56 + - 080fd5739bb4 tool_panel_section_label: RSeQC tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/sambam.yml b/usegalaxy.org.au/sambam.yml index 11c6e49ed..29079f86b 100644 --- a/usegalaxy.org.au/sambam.yml +++ b/usegalaxy.org.au/sambam.yml @@ -2,18 +2,18 @@ tools: - name: bam_to_sam owner: devteam revisions: - - 3c661e57a88f - 10184eaa85fc + - 3c661e57a88f - 88eedb4abea0 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_filter owner: devteam revisions: - - 1dfd95ee241e - - 993b19f20c76 - cb20f99fd45b + - 993b19f20c76 - 108db6635177 + - 1dfd95ee241e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools_split_mapped @@ -32,8 +32,8 @@ tools: - name: bamtools_split_tag owner: iuc revisions: - - e30af4e78cd3 - e9b9c489aacc + - e30af4e78cd3 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: bamtools @@ -75,17 +75,17 @@ tools: - name: qualimap_bamqc owner: iuc revisions: - - e7fd6754d093 + - 19ece8afbaab - 5f8e69cc4c6e + - e7fd6754d093 - 30a201c9c310 - - 19ece8afbaab tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: qualimap_multi_bamqc owner: iuc revisions: - - e38af83df163 - 17b35d23731f + - e38af83df163 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: sam2interval @@ -123,25 +123,25 @@ tools: - name: samtool_filter2 owner: devteam revisions: - - 649a225999a5 - 56c31114ad4a + - 649a225999a5 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_bedcov owner: devteam revisions: - - 46c6639921f1 - 9149ad20699a - 6856f8a01905 + - 46c6639921f1 - 12749212f61b tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_calmd owner: devteam revisions: + - 06dc50b7b711 - 33208952b99d - 92ec40abcdcf - - 06dc50b7b711 - 26b4f9f98aca tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu @@ -160,38 +160,38 @@ tools: - name: samtools_fastx owner: iuc revisions: - - b3d99709fe1a - - 720217c23995 - a8d69aee190e - 66e23b11feae - b906586a6596 + - 720217c23995 + - b3d99709fe1a tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_fixmate owner: iuc revisions: - - e5ece8fa99de - d2df79922531 + - e5ece8fa99de tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_flagstat owner: devteam revisions: - - cc61ade70eb8 - fe34990e5ce7 + - cc61ade70eb8 + - fefd89ab563c - 22970df7a40e - db17d5321bad - - fefd89ab563c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_idxstats owner: devteam revisions: - - fa5d3e61e429 - - 7a6034296ae9 - - 88b8c2916784 - 811fc2d75ad4 - 7def34e6cf4d + - 7a6034296ae9 + - fa5d3e61e429 + - 88b8c2916784 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_markdup @@ -204,8 +204,8 @@ tools: - name: samtools_merge owner: iuc revisions: - - cae2794d2deb - b40e2d865d52 + - cae2794d2deb - 65a38e8c8e2a - 36677f429310 - 740ce0a18f0d @@ -214,27 +214,27 @@ tools: - name: samtools_mpileup owner: devteam revisions: - - 583abf29fc8e - - 9da0311ab1dd - - 329deb17a9f7 - b61f5d6a7f25 - 8da515fbc1bf + - 329deb17a9f7 + - 583abf29fc8e + - 9da0311ab1dd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_phase owner: devteam revisions: - - 1e5880498f52 - b5c3b1856370 + - 1e5880498f52 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_reheader owner: devteam revisions: - 30388d878f81 + - bb8cfc6f6e0c - db000c6007a0 - 85e38b31e8b3 - - bb8cfc6f6e0c tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_rmdup @@ -246,54 +246,54 @@ tools: - name: samtools_slice_bam owner: devteam revisions: - - a4a10c7924d1 - b8beef827165 + - a4a10c7924d1 - 344fc91e1bfd tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_sort owner: devteam revisions: - - e613c1ad4c4c - - cab3f8d35989 - 6c2c1836728b + - cab3f8d35989 + - e613c1ad4c4c - d54a4df48867 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_split owner: devteam revisions: - - 5d9ae78f34d3 - - bcedabb53ddf - - bd850490c7f1 - - 135c85f4cfaf - 818030fa6bbf - b7f7826ef1cd + - bcedabb53ddf + - 5d9ae78f34d3 + - 135c85f4cfaf + - bd850490c7f1 tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_stats owner: devteam revisions: - - 1cc79f49b8d5 - - 145f6d74ff5e - - 24c5d43cb545 - - 541082d03bef - 3a0efe14891f + - 541082d03bef + - 24c5d43cb545 + - 1cc79f49b8d5 - 5a08c09b9311 + - 145f6d74ff5e tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu - name: samtools_view owner: iuc revisions: - - 6be888be75f9 - - bf328cec6a42 - - 5826298f6a73 + - b72793637686 - 2dce91e11ca7 + - bf328cec6a42 + - 0dbf49c414ae + - 6be888be75f9 - c370440f901e - - 32dc5f781059 + - 5826298f6a73 - 350bbc5c2ffd + - 32dc5f781059 - b01db2684fa5 - - b72793637686 - - 0dbf49c414ae tool_panel_section_label: SAM/BAM tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/send_data.yml b/usegalaxy.org.au/send_data.yml index 32e52de63..fbc135542 100644 --- a/usegalaxy.org.au/send_data.yml +++ b/usegalaxy.org.au/send_data.yml @@ -8,13 +8,13 @@ tools: - name: ena_upload owner: iuc revisions: - - ea5e944f447d + - a62c4a11a67d - d147d6455873 + - 480d9e9d156b + - ea5e944f447d - 5cb6146337d8 - 4aab5ae907b6 - - 480d9e9d156b - - 6f6537780379 - 59bb6d34fca6 - - a62c4a11a67d + - 6f6537780379 tool_panel_section_label: Send Data tool_shed_url: toolshed.g2.bx.psu.edu diff --git a/usegalaxy.org.au/single_cell.yml b/usegalaxy.org.au/single_cell.yml index 38e972f19..1e9de4518 100644 --- a/usegalaxy.org.au/single_cell.yml +++ b/usegalaxy.org.au/single_cell.yml @@ -9,9 +9,9 @@ tools: owner: bgruening revisions: - ecb9ea6269ee - - f2000bc73102 - e4c01dcece8b - e32b215b7c04 + - f2000bc73102 - b0fe3e482cb7 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -19,45 +19,45 @@ tools: owner: iuc revisions: - 707023fa62fe + - c0b037b12765 - e1c3c2f2a834 - 7a6655aa6eb2 - - c0b037b12765 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_import owner: iuc revisions: - - 00712416fdaa - - 55e35e9203cf - - cfc3f5a57dc6 - - fb9e030ffae4 - 93dd15e13e6a - 32e547223c9e + - fb9e030ffae4 + - cfc3f5a57dc6 + - 55e35e9203cf - 6f143dfe902a + - 00712416fdaa tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_inspect owner: iuc revisions: - - 14c576ea6148 - - 6f0d0c784f09 + - 038e32885fec - 39e945f0b2c1 - b9fac48532eb - - 688357ad5e61 + - 6f0d0c784f09 - ee98d611afc6 - - 038e32885fec + - 14c576ea6148 + - 688357ad5e61 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_manipulate owner: iuc revisions: - - c4209ea387d4 - - d4af736e7b83 - - b85871dd69f9 - - 3d748954434b - 9bd945a03d7b - 43cb7b5a6fe7 - ed4996a16f7f + - c4209ea387d4 + - d4af736e7b83 + - 3d748954434b + - b85871dd69f9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: anndata_ops @@ -71,37 +71,37 @@ tools: - name: baredsc_1d owner: iuc revisions: + - 0e70b2dfe4be - 769d815e4b0d - 02b1fe7aed76 - - 0e70b2dfe4be - 4fff5a293013 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_2d owner: iuc revisions: + - a90f8efe08b4 + - 344c2af50552 - aa4a6f0916b4 - c29e7bb492bf - - 344c2af50552 - - a90f8efe08b4 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_1d owner: iuc revisions: - - b13d3e4c48e1 - 5b7c81b35b89 - - 050cf43887d3 - c32347702e12 + - 050cf43887d3 + - b13d3e4c48e1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: baredsc_combine_2d owner: iuc revisions: - - ae969fdb8442 - 239193b96d72 - - 02fc39c8610d - 1d77986f9ddc + - 02fc39c8610d + - ae969fdb8442 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: cell_intensity_processing @@ -137,11 +137,11 @@ tools: - name: dropletutils owner: iuc revisions: - - cfe1e6c28d95 - a9caad671439 - cdf4443d5625 - - 8855361fcfc5 + - cfe1e6c28d95 - 2c1200fba922 + - 8855361fcfc5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: episcanpy_build_matrix @@ -171,33 +171,33 @@ tools: - name: hicexplorer_chicaggregatestatistic owner: bgruening revisions: - - 01c37e54e86e - - fb7068d30ec9 - 952abbc4b1de + - fb7068d30ec9 + - 01c37e54e86e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicdifferentialtest owner: bgruening revisions: + - 57aeaf6b237d - 9d42a6133690 - f1c35f3f310d - - 57aeaf6b237d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicexportdata owner: bgruening revisions: - - 23b8d6b8960c - - 163fd744e235 - cab616fe7e64 + - 163fd744e235 + - 23b8d6b8960c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicplotviewpoint owner: bgruening revisions: - - b9ab56aecd18 - - f47ac4a0b337 - 013e53ccc7ac + - f47ac4a0b337 + - b9ab56aecd18 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicqualitycontrol @@ -211,16 +211,16 @@ tools: - name: hicexplorer_chicsignificantinteractions owner: bgruening revisions: - - f8320df1866b - 640e0e45518a - 45a386d18509 + - f8320df1866b tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_chicviewpointbackgroundmodel owner: bgruening revisions: - - f963c251ac77 - c354255ff705 + - f963c251ac77 - 9d02f1819e81 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -235,24 +235,24 @@ tools: - name: hicexplorer_hicadjustmatrix owner: bgruening revisions: - - e06265d204f6 - 782bdcb775fb - 2dccb6bb0add + - e06265d204f6 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaggregatecontacts owner: bgruening revisions: - b05f662f9f35 - - 63c8377c58b3 - f0216498a666 + - 63c8377c58b3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicaverageregions owner: bgruening revisions: - - 8a11d70b6cd8 - fe3aa71590d5 + - 8a11d70b6cd8 - c72fa6cb8817 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -267,32 +267,32 @@ tools: - name: hicexplorer_hiccompartmentspolarization owner: bgruening revisions: + - 4401ed529d2c - a315574104c6 - 3a6a5381db36 - - 4401ed529d2c tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicconvertformat owner: bgruening revisions: - - c0737631eea1 - 2ba6cee8e4db - a83732c79949 + - c0737631eea1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrectmatrix owner: bgruening revisions: - - 62b720dceb56 - - ea19190ce5e0 - 30d7390bc918 + - ea19190ce5e0 + - 62b720dceb56 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hiccorrelate owner: bgruening revisions: - - cd40ca76865a - 2786a931cad2 + - cd40ca76865a - 2b4d6a8dab36 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -307,24 +307,24 @@ tools: - name: hicexplorer_hicdifferentialtad owner: bgruening revisions: + - 77d8e0fd162a - 5dfba24d7bdd - 07dd436ea686 - - 77d8e0fd162a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicfindrestrictionsites owner: bgruening revisions: + - 6c5097f6d41e - f1b3902f8baf - 972dcccb5bbc - - 6c5097f6d41e tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hichyperoptdetectloops owner: bgruening revisions: - - 409396ea5cf0 - bb8849fca57c + - 409396ea5cf0 - 7f7c6ead2d0d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -332,40 +332,40 @@ tools: owner: bgruening revisions: - e4f8fceab96a - - b0f33533181d - 51e40e9b6c3c + - b0f33533181d tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicinterintratad owner: bgruening revisions: + - 32173084d53f - 55b013e59018 - c261b6b05ee3 - - 32173084d53f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergedomains owner: bgruening revisions: - - b6b8c8672756 - - 4b194e675916 - b376ef118807 + - 4b194e675916 + - b6b8c8672756 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicmergeloops owner: bgruening revisions: - 910c6a1c3a27 - - 1511a8ebe906 - ed900cd4a0a9 + - 1511a8ebe906 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicnormalize owner: bgruening revisions: - f34ab9882252 - - 2aa5b6b65197 - 6d042c96aceb + - 2aa5b6b65197 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotaverageregions @@ -379,9 +379,9 @@ tools: - name: hicexplorer_hicplotdistvscounts owner: bgruening revisions: - - 11f39d7f6c64 - - 06ced663d24f - 6326cd29c1c3 + - 06ced663d24f + - 11f39d7f6c64 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicplotsvl @@ -403,17 +403,17 @@ tools: - name: hicexplorer_hicquickqc owner: bgruening revisions: - - 21d859ad4502 - - 5cbd7a902a8d - ea8fb5e899e8 + - 5cbd7a902a8d + - 21d859ad4502 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hicsummatrices owner: bgruening revisions: + - f81750434d70 - 1d6af10874d5 - 36dfa2825a59 - - f81750434d70 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: hicexplorer_hictadclassifier @@ -439,20 +439,20 @@ tools: - name: hicexplorer_hicvalidatelocations owner: bgruening revisions: - - 11a3385e03b5 - - cef9fb4ece1c - 1d201e8378b3 + - cef9fb4ece1c + - 11a3385e03b5 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: modify_loom owner: iuc revisions: + - 59be31ac9dc3 + - 4b0adaa31c95 - 7784821452ac - db575b4c8b22 - eeab712b0b99 - - 59be31ac9dc3 - e98619de2776 - - 4b0adaa31c95 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_compare @@ -464,16 +464,16 @@ tools: - name: music_construct_eset owner: bgruening revisions: - - 2cfd0db49bbc - 48f0fb3061b1 - 7ffaa0968da3 + - 2cfd0db49bbc tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_deconvolution owner: bgruening revisions: - - 56371b5a2da9 - 8cd2ecfa2e61 + - 56371b5a2da9 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: music_inspect_eset @@ -498,20 +498,20 @@ tools: - name: raceid_clustering owner: iuc revisions: - - 49776718ae90 - - 7e014059a88d + - a4b734cd253b - c4f39bf4a068 - f911a64454fb - - a4b734cd253b + - 7e014059a88d + - 49776718ae90 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_filtnormconf owner: iuc revisions: - 8b917923f7d4 + - d45f092caf24 - 43c146e25a43 - 7608d5faee41 - - d45f092caf24 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: raceid_inspectclusters @@ -525,8 +525,8 @@ tools: - name: raceid_inspecttrajectory owner: iuc revisions: - - df8e4e54d367 - 6e90c8adf84f + - df8e4e54d367 - 69018f285aa3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu @@ -534,10 +534,10 @@ tools: owner: iuc revisions: - 44b935f2271b - - e93b008c637a - 72979cac22b2 - - 2bfd55b87af3 - c92d0f9338c5 + - 2bfd55b87af3 + - e93b008c637a tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: run_sccaf @@ -555,111 +555,111 @@ tools: - name: scanpy_cluster_reduce_dimension owner: iuc revisions: + - 38db3fef7aad + - 6acb08931836 - 4d8f983cd751 - - cb43c5d3acd3 - 8983e7a04ba7 + - 6f83f8fd381f - aaa5da8e73a9 - 77b91b9bdf52 - - 38db3fef7aad - - 6f83f8fd381f - - 6acb08931836 - - b2df381a6004 - f9353ee6a0d4 + - b2df381a6004 + - cb43c5d3acd3 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_filter owner: iuc revisions: - 3c86f71498bc - - a97abb8cd15b - - fc0321c000a3 - - 64388be6d510 + - b409c2486353 - 72a6bebab2a5 - 277313130da5 + - fc0321c000a3 + - 8cb783c81905 - a03ff8633507 + - a97abb8cd15b + - 64388be6d510 - d636ce5cde16 - - 8cb783c81905 - - b409c2486353 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_inspect owner: iuc revisions: + - 18262103fa61 - c0a80a16560f - d86cb2ce311b - - f54f0f0598ad + - 5e9171dc8244 + - c5d3684f7c4c + - 3081ff5c84a3 - 5c3ebe2adc77 + - f54f0f0598ad - 6c145a6868cc - - 3081ff5c84a3 - - c5d3684f7c4c - - 18262103fa61 - 6bd82ed14acd - - 5e9171dc8244 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_normalize owner: iuc revisions: - - 4bda4412b8c2 - - a407e7f8bdc1 + - ab55fe8030b6 + - 56c0d4acef02 - 9f354c7c8c92 - c9cb76cf8d6c - - 146ae5d70b47 - - d844935c906c + - a407e7f8bdc1 - 7b9fafe32c86 + - 4bda4412b8c2 - 94c19fb1281c - - ab55fe8030b6 - 3bcd5445cd7a - - 56c0d4acef02 + - d844935c906c + - 146ae5d70b47 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_plot owner: iuc revisions: - - 40812a65a78b - - f7446fd8d5e7 - - 95777145cb92 - - 0185bd174ea0 - 9b0cdb8cf6be - - 62acdd96d4a0 - 7647e5cd1b8b - - 6adf98e782f3 - aa0c474463c2 + - 40812a65a78b + - 62acdd96d4a0 + - 6adf98e782f3 + - 95777145cb92 + - 0185bd174ea0 + - f7446fd8d5e7 - 1072ce66b426 - - 6f5349dd5c49 - dbbe1ea8ecb1 + - 6f5349dd5c49 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scanpy_remove_confounders owner: iuc revisions: - - c65fce500915 - - c5541bfb8feb - fe8f16c594ec - - 9fb627495ec2 + - 215733a383f2 - 458e8f43a775 - - f2f6c703da06 - - d18e7a6e5cd4 - a39040ae0a38 + - c65fce500915 + - 9fb627495ec2 - 73ab2ac53d06 + - d18e7a6e5cd4 - bf2017df9837 - - 215733a383f2 + - c5541bfb8feb + - f2f6c703da06 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_create_qcmetric_ready_sce owner: iuc revisions: - 8f333f90d8d6 - - fd808de478b1 - b834074a9aff + - fd808de478b1 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_filter owner: iuc revisions: + - 652923ce664f - b7ea9f09c02f - 7a365ec81b52 - - 652923ce664f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_normalize @@ -672,8 +672,8 @@ tools: owner: iuc revisions: - 81e5bdff4853 - - 2e41b35b5bdd - ef4c80837bc5 + - 2e41b35b5bdd tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_exprs_freq @@ -685,9 +685,9 @@ tools: - name: scater_plot_pca owner: iuc revisions: - - 9e5c0bb18d08 - c99ba278dfa9 - 46fc6751d746 + - 9e5c0bb18d08 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: scater_plot_tsne @@ -909,8 +909,8 @@ tools: - name: sinto_barcode owner: iuc revisions: - - d1b34ac42b8f - fb61eb03e313 + - d1b34ac42b8f tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: sinto_fragments @@ -943,8 +943,8 @@ tools: - name: snapatac2_plotting owner: iuc revisions: - - 05bd4db20227 - fecf9664c885 + - 05bd4db20227 tool_panel_section_label: Single-cell tool_shed_url: toolshed.g2.bx.psu.edu - name: snapatac2_preprocessing diff --git a/usegalaxy.org.au/statistics.yml b/usegalaxy.org.au/statistics.yml index 18c1d1305..cffa3f0e0 100644 --- a/usegalaxy.org.au/statistics.yml +++ b/usegalaxy.org.au/statistics.yml @@ -33,8 +33,8 @@ tools: owner: iuc revisions: - 4c07ddedc198 - - 562f3c677828 - 419027d822d6 + - 562f3c677828 - 2f3c6f2dcf39 - 746e8e4bf929 tool_panel_section_label: Statistics @@ -42,8 +42,8 @@ tools: - name: dwt_cor_ava_perclass owner: devteam revisions: - - a0defff5cf89 - b87bbe6bc044 + - a0defff5cf89 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_cor_avb_all @@ -56,8 +56,8 @@ tools: - name: dwt_ivc_all owner: devteam revisions: - - 0b89b03ad760 - 506ae7b0d85d + - 0b89b03ad760 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: dwt_var_perclass @@ -70,9 +70,9 @@ tools: - name: dwt_var_perfeature owner: devteam revisions: + - cb1c59d69557 - 6c29c7e347e8 - 7a15159140d1 - - cb1c59d69557 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: generate_pc_lda_matrix @@ -114,40 +114,40 @@ tools: - name: sklearn_build_pipeline owner: bgruening revisions: - - b1eda492f063 - 4c4ec859c31a - - 840f29aad145 - - 7442b94d6a1e - 9c3e1d3235c8 + - 840f29aad145 - aef56d0e7a61 + - 7442b94d6a1e + - b1eda492f063 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_estimator_attributes owner: bgruening revisions: - - 30d21a6041f6 - d0352e8b4c10 - - 9fda0b82f419 - 375bbd555f4a + - 9fda0b82f419 + - 30d21a6041f6 - 07843f917990 tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_nn_classifier owner: bgruening revisions: + - 4cc980df6265 - 8b1b2b91f8d0 + - 2c58b83c9bad - 7ae443e6217d - - 4cc980df6265 - cd02bf168d23 - - 2c58b83c9bad tool_panel_section_label: Statistics tool_shed_url: toolshed.g2.bx.psu.edu - name: sklearn_numeric_clustering owner: bgruening revisions: - 4bbaf77573ef - - 1dd433d2c92c - bb9fc9d46ea4 + - 1dd433d2c92c - ad7e0b4291ee - e10e776f2109 - 7dd3fb35904f diff --git a/usegalaxy.org.au/text_manipulation.yml b/usegalaxy.org.au/text_manipulation.yml index f5da5abf5..309154426 100644 --- a/usegalaxy.org.au/text_manipulation.yml +++ b/usegalaxy.org.au/text_manipulation.yml @@ -34,14 +34,14 @@ tools: - name: column_maker owner: devteam revisions: - - 464b9305180e - - 6e8d94597139 - - be25c075ed54 - - 9cd341095afd - 13b6f0007d9e + - aff5135563c6 + - 6e8d94597139 + - 464b9305180e - 6595517c2dd8 + - be25c075ed54 - 02026300aa45 - - aff5135563c6 + - 9cd341095afd tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: column_remove_by_header @@ -53,8 +53,8 @@ tools: - name: concatenate_multiple_datasets owner: artbio revisions: - - 6f54dc6b37da - 3a4694d4354f + - 6f54dc6b37da tool_panel_section_label: Text Manipulation tool_shed_url: toolshed.g2.bx.psu.edu - 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