Merge pull request #413 from RECETOX/hechth/issue412

bumped galaxy version in all wrapers to trigger toolshed update
RECETOX · Oct 12, 2023 · b1cc1ae · b1cc1ae
2 parents 97249a1 + 9b547e4
commit b1cc1ae
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diff --git a/tools/biotransformer/biotransformer.xml b/tools/biotransformer/biotransformer.xml
@@ -1,4 +1,4 @@
-<tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,7 +7,7 @@
         <xref type="bio.tools">biotransformer</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement>
+        <requirement type="package" version="3.0_20230403">biotransformer</requirement>
         <requirement type="package" version="3.1.1">openbabel</requirement>
         <requirement type="package" version="1.1.1">pandas</requirement>
     </requirements>
@@ -59,19 +59,19 @@
             <param name="input_file" value="smiles.csv"/>
             <output name="output_file">
                 <assert_contents>
-                    <has_size value="8600" delta="100"/>
+                    <has_size value="8600" delta="300"/>
                     <has_n_lines n="225" delta="10"/>
                 </assert_contents>
             </output>
             <output name="output_file2">
                 <assert_contents>
-                    <has_size value="8600" delta="100"/>
+                    <has_size value="8600" delta="300"/>
                     <has_n_lines n="225" delta="10"/>
                 </assert_contents>
             </output>
             <output name="output_file3">
                 <assert_contents>
-                    <has_size value="7400" delta="100"/>
+                    <has_size value="7400" delta="300"/>
                     <has_n_lines n="186" delta="10"/>
                 </assert_contents>
             </output>

diff --git a/tools/biotransformer/macros.xml b/tools/biotransformer/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.0_20230403</token>
+    <token name="@TOOL_VERSION@">3.0.20230403</token>
     <xml name="creator">
         <creator>
             <person

diff --git a/tools/matchms/matchms_add_key.xml b/tools/matchms/matchms_add_key.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>Set metadata key in MSP to static value</description>
 
     <macros>

diff --git a/tools/matchms/matchms_convert.xml b/tools/matchms/matchms_convert.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy1" profile="21.05">
+<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="21.05">
     <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
 
     <macros>

diff --git a/tools/matchms/matchms_filtering.xml b/tools/matchms/matchms_filtering.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>filter and normalize mass spectrometry data</description>
 
     <macros>

diff --git a/tools/matchms/matchms_fingerprint_similarity.xml b/tools/matchms/matchms_fingerprint_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_fingerprint_similarity" name="matchms fingerprint similarity" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_fingerprint_similarity" name="matchms fingerprint similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors</description>
 
     <macros>

diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>reformat scores object of matchms to long format table</description>
 
     <macros>

diff --git a/tools/matchms/matchms_metadata_export.xml b/tools/matchms/matchms_metadata_export.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>extract all metadata from mass spectra file to tabular format</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/matchms/matchms_metadata_match.xml b/tools/matchms/matchms_metadata_match.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_metadata_match" name="matchms metadata match" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>matchms metadata match calculation for numeric fields based on tolerance</description>
 
     <macros>

diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>create similarity network graph from matchms similarity scores</description>
 
     <macros>

diff --git a/tools/matchms/matchms_similarity.xml b/tools/matchms/matchms_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_similarity" name="matchms similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>calculate the similarity score and matched peaks</description>
 
     <macros>

diff --git a/tools/matchms/matchms_spectral_similarity.xml b/tools/matchms/matchms_spectral_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_spectral_similarity" name="matchms spectral similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>matchms spectral similarity calculation</description>
 
     <macros>

diff --git a/tools/matchms/matchms_split.xml b/tools/matchms/matchms_split.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>split a large library into subsets</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/msmetaenhancer/msmetaenhancer.xml b/tools/msmetaenhancer/msmetaenhancer.xml
@@ -1,4 +1,4 @@
-<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy2">
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy3">
     <description>annotate MS data</description>
 
     <macros>

diff --git a/tools/mzml_validator/mzml_validator.xml b/tools/mzml_validator/mzml_validator.xml
@@ -1,4 +1,4 @@
-<tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy1" profile="21.05">
+<tool id="mzml_validator" name="mzML Schema Validator" version="0.1.0+galaxy2" profile="21.05">
     <description>validates mzML files against XML Schema Definition (XSD)</description>
     <creator>
         <person

diff --git a/tools/ramclustr/ramclustr.xml b/tools/ramclustr/ramclustr.xml
@@ -1,4 +1,4 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2" profile="21.09">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy3" profile="21.09">
     <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/ramclustr/ramclustr_define_experiment.xml b/tools/ramclustr/ramclustr_define_experiment.xml
@@ -1,4 +1,4 @@
-<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy1" profile="21.09">
+<tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy2" profile="21.09">
     <description>Definition of experimental design used for record keeping and writing spectra data.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_msfinder/.shed.yml b/tools/recetox_msfinder/.shed.yml
@@ -6,6 +6,13 @@ categories:
 repositories:
   recetox_msfinder:
     description: "MS-FINDER is program for compound annotation for EI-MS (GC/MS) and MS/MS data"
+    long_description: |
+      "Molecular formulas of precursor ions are determined from accurate mass, 
+      isotope ratio, and product ion information. All isomer structures of the 
+      predicted formula are retrieved from metabolome databases and MS/MS 
+      fragmentations are predicted in silico. The structures are ranked by a 
+      combined weighting score considering bond dissociation energies, mass accuracies, 
+      fragment linkages and, most importantly, nine HR rules.""
     include:
       - recetox_msfinder.xml
       - macros.xml

diff --git a/tools/recetox_msfinder/macros.xml b/tools/recetox_msfinder/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">v3.5.2-rcx0</token>
+    <token name="@TOOL_VERSION@">v3.5.2</token>
     <xml name="requirements">
         <requirements>
             <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx0</container>

diff --git a/tools/recetox_msfinder/recetox_msfinder.xml b/tools/recetox_msfinder/recetox_msfinder.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy0">
+<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy1">
     <description>Annotation of fragment peaks in mass spectral libraries.</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/recetox_xmsannotator/.shed.yml b/tools/recetox_xmsannotator/.shed.yml
@@ -6,6 +6,11 @@ categories:
 repositories:
   recetox_xmsannotator_advanced:
     description: "Annotate peak table using RT, m/z and mass defect based clustering, isotopic patterns, pathways and chemical score computation"
+    long_description: |
+      "Annotate peak table using RT, m/z and mass defect based clustering, isotopic patterns, pathways and chemical score computation.
+      This tool is an advanced version of the original xMSannotator tool.
+      It is based on the same principles, but it is more flexible and implements a new isotopic pattern matching.
+      It also allows to use different databases for different compounds."
     include:
       - recetox_xmsannotator_advanced.xml
       - macros.xml

diff --git a/tools/recetox_xmsannotator/recetox_xmsannotator_advanced.xml b/tools/recetox_xmsannotator/recetox_xmsannotator_advanced.xml
@@ -1,4 +1,4 @@
-<tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy0">
+<tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy1">
 
     <description>annotate peak intensity table including scores and confidence levels</description>
     <macros>

diff --git a/tools/retip/retip_apply.xml b/tools/retip/retip_apply.xml
@@ -1,4 +1,4 @@
-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3">
+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy4">
     <description>is retention time predictor for Metabolomics</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/retip/retip_descriptors.xml b/tools/retip/retip_descriptors.xml
@@ -1,4 +1,4 @@
-<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy3">
+<tool id="retip_descriptors" name="Retip chemical descriptors" version="@TOOL_VERSION@+galaxy4">
     <description>for retention time prediction</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/retip/retip_filter_rt.xml b/tools/retip/retip_filter_rt.xml
@@ -1,4 +1,4 @@
-<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy3">
+<tool id="retip_filter_rt" name="Retip filter" version="@TOOL_VERSION@+galaxy4">
     <description>for predicted RT's</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/retip/retip_train.xml b/tools/retip/retip_train.xml
@@ -1,4 +1,4 @@
-<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy3">
+<tool id="retip_train" name="Retip training" version="@TOOL_VERSION@+galaxy4">
     <description>the Keras model to predict retention times</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/riassigner/.shed.yml b/tools/riassigner/.shed.yml
@@ -6,7 +6,9 @@ categories:
 repositories:
   riassigner:
     description: "RIAssigner is a python tool for retention index (RI) computation for GC-MS data."
-
+    long_description: |
+      "RIAssigner is a python tool for retention index (RI) computation for GC-MS data.
+      Supported input data are msp and csv. Supported computational methods are piecewise linear interpolation and b-Spline interpolation."
     include:
       - riassigner.xml
       - macros.xml

diff --git a/tools/riassigner/riassigner.xml b/tools/riassigner/riassigner.xml
@@ -1,4 +1,4 @@
-<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy3" profile="21.09">
+<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy4" profile="21.09">
     <description>compute retention indices</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/rmassbank/rmassbank.xml b/tools/rmassbank/rmassbank.xml
@@ -1,4 +1,4 @@
-<tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy2">
+<tool id="rmassbank" name="RMassBank" version="@TOOL_VERSION@+galaxy3">
     <macros>
         <import>macros.xml</import>
     </macros>

diff --git a/tools/spec2vec/.shed.yml b/tools/spec2vec/.shed.yml
@@ -1,19 +1,17 @@
+name: spec2vec
 owner: recetox
 remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec"
 homepage_url: "https://github.com/iomega/spec2vec"
 categories:
   - Metabolomics
-repositories:
-  spec2vec_training:
-    description: "Train a Spec2Vec model for mass spectra similarity scoring."
-    include:
-      - spec2vec_training.xml
-      - macros.xml
-      - spec2vec_training_wrapper.py
-      - test-data
-  spec2vec_similarity:
-    description: "Mass spectra similarity scoring using a trained Spec2Vec model."
-    include:
-      - spec2vec_similarity.xml
-      - macros.xml
-      - test-data
+description: "Mass spectra similarity scoring using a trained Spec2Vec model."
+long_description: |
+  "Spec2Vec is a novel spectral similarity score inspired by a natural language processing algorithm—Word2Vec.
+  Spec2Vec learns frag- mental relationships within a large set of spectral data to derive abstract spectral 
+  embeddings that can be used to assess spectral similarities."auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+description_template: "{{ tool_name }} tool from the spec2vec package"
+suite:
+  name: suite_spec2vec
+  description: tools from the spec2vec suite are used for searching mass spectral libraries and training a Spec2Vec model.
+  type: repository_suite_definition
diff --git a/tools/spec2vec/macros.xml b/tools/spec2vec/macros.xml
@@ -28,16 +28,18 @@
 
     <xml name="input_param">
         <conditional name="scores">
-            <param name="use_scores" label="Use Scores Object" type="boolean" truevalue="TRUE" falsevalue="FALSE"
-                   checked="false"/>
-            <when value="TRUE">
+            <param name="use_scores" label="Use Scores Object" type="select">
+                <option value="False" selected="true">FALSE</option>
+                <option value="True">TRUE</option>
+            </param>
+            <when value="True">
                 <param label="Scores object" name="scores_in" type="data" format="json"
                     help="Scores objects calculated previously using one of the matchms similarity tools." />
             </when>
-            <when value="FALSE">
-                <param label="Queries spectra" name="queries" type="data" format="msp,mgf"
+            <when value="False">
+                <param label="Queries spectra" name="queries" type="data" format="msp"
                     help="Query mass spectra to match against references."/>
-                <param label="Reference spectra" name="references" type="data" format="msp,mgf"
+                <param label="Reference spectra" name="references" type="data" format="msp"
                     help="Reference mass spectra to match against as library."/>
             </when>
         </conditional>
@@ -52,8 +54,8 @@
 <token name="@init_scores@">
 from matchms.importing import load_from_msp, scores_from_json
 from matchms import Scores
-#if $scores.use_scores
-scores = scores_from_json("$scores_in")
+#if $scores.use_scores == "True"
+scores = scores_from_json("${scores_in}")
 #else
 scores = Scores(references=list(load_from_msp("$references")), queries=list(load_from_msp("$queries")), is_symmetric=False)
 #end if

diff --git a/tools/spec2vec/spec2vec_similarity.xml b/tools/spec2vec/spec2vec_similarity.xml
@@ -1,4 +1,4 @@
-<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="spec2vec_similarity" name="spec2vec similarity" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -63,6 +63,7 @@ scores.to_json("$similarity_scores")
 
     <tests>
         <test> <!-- TEST #1: Test Spec2Vec. -->
+            <param name="use_scores" value="False"/>
             <param name="references" value="inp_filtered_library.msp" ftype="msp"/>
             <param name="queries" value="inp_filtered_spectra.msp" ftype="msp"/>
             <param name="model_metadata" value="model_100.json" ftype="json"/>

diff --git a/tools/spec2vec/spec2vec_training.xml b/tools/spec2vec/spec2vec_training.xml
@@ -1,4 +1,4 @@
-<tool id="spec2vec_training" name="spec2vec model training" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="spec2vec_training" name="spec2vec model training" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>Train a Spec2Vec model for mass spectra similarity scoring</description>
 
     <macros>

diff --git a/tools/waveica/waveica.xml b/tools/waveica/waveica.xml
@@ -1,4 +1,4 @@
-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy3" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy4" python_template_version="3.5">
     <description>removal of batch effects for untargeted metabolomics data</description>
     <macros>
         <import>macros.xml</import>

diff --git a/tools/waveica/waveica_wrapper.R b/tools/waveica/waveica_wrapper.R
@@ -109,8 +109,7 @@ waveica_singlebatch <- function(file,
 
   data <- sort_by_injection_order(data)
 
-  feature_columns <- colnames(data)[!colnames(data) %in%
-    c(required_columns, optional_columns)]
+  feature_columns <- colnames(data)[!colnames(data) %in% c(required_columns, optional_columns)]
   features <- data[, feature_columns]
   injection_order <- data$injectionOrder
 
@@ -137,14 +136,9 @@ waveica_singlebatch <- function(file,
 
 sort_by_injection_order <- function(data) {
   if ("batch" %in% colnames(data)) {
-    data <- data[order(data[, "batch"],
-      data[, "injectionOrder"],
-      decreasing = FALSE
-    ), ]
+    data <- data[order(data[, "batch"], data[, "injectionOrder"], decreasing = FALSE), ]
   } else {
-    data <- data[order(data[, "injectionOrder"],
-      decreasing = FALSE
-    ), ]
+    data <- data[order(data[, "injectionOrder"], decreasing = FALSE), ]
   }
   return(data)
 }

diff --git a/tools/xtb/xtb_molecular_optimization.xml b/tools/xtb/xtb_molecular_optimization.xml
@@ -1,4 +1,4 @@
-<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="xtb_molecular_optimization" name="xtb molecular optimization" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>Semiempirical quantum mechanical molecular optimization method</description>
     <macros>
         <import>macros.xml</import>