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manifest_GSEA2
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manifest_GSEA2
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#GSEA2
#Mon Aug 14 17:11:37 UTC 2023
JVMLevel=
LSID=urn\:lsid\:genepattern.org\:module.analysis\:00438\:1.8
author=Anthony Castanza, Edwin Huang;Mesirov Lab UCSD
commandLine=python3 <libdir>run.gsea2.py --libdir\=<libdir> <expression.dataset> <gene.sets.database> <number.of.permutations> <phenotype.labels> <reverse.phenotypes> <permutation.type> <collapse.dataset> <chip.platform.file> <metric.for.ranking.genes> <enrichment.algorithm> <weighting.exponent> <max.gene.set.size> <min.gene.set.size> <seed.for.permutation> <override.gene.list.length.validation> <plot.graphs> --cpu\=<job.cpuCount>
cpuType=any
description=New GSEA (GSEA.jl 0.17.3 Build)
documentationUrl=https\://github.com/KwatMDPhD/GSEA.jl
fileFormat=
job.cpuCount=3
job.docker.image=acastanza/gsea2\:0.17.3
job.memory=
job.walltime=
language=any
name=GSEA2
os=any
p10_MODE=
p10_TYPE=TEXT
p10_default_value=ks
p10_description=Which algorithm to use for running GSEA the old Kolmogorov-Smirnov enrichment statistic (Classic GSEA), an "area under the curve" variant of the Kolmogorov-Smirnov enrichment statistic, or, or the next-generation "kli, kliom, or kliop" GSEA methods.
p10_fileFormat=
p10_flag=--alg\=
p10_name=enrichment.algorithm
p10_numValues=1..1
p10_optional=
p10_prefix=--alg\=
p10_prefix_when_specified=--alg\=
p10_type=java.lang.String
p10_value=ks\=Kolmogorov-Smirnov (Classic GSEA);ksa\=Kolmogorov-Smirnov Area;kli\=KLI;kliom\=KLIOM;kliop\=KLIOP
p11_MODE=
p11_TYPE=Floating Point
p11_default_value=1
p11_description=Exponent for weighting the Kolmogorov-Smirnov or Kolmogorov-Smirnov Area enrichment method.<br>\nSetting 1.0 is equivalent to the old "scoring scheme\=weighted" option.<br> \nSetting 0 when running the Kolmogorov-Smirnov enrichment method is equivalent to the unweighted Kolmogorov-Smirnov statistic ("scoring scheme\=classic" option in prior versions of GSEA)
p11_fileFormat=
p11_flag=--exponent\=
p11_name=weighting.exponent
p11_numValues=1..1
p11_optional=
p11_prefix=--exponent\=
p11_prefix_when_specified=--exponent\=
p11_type=java.lang.Float
p11_value=
p12_MODE=
p12_TYPE=Integer
p12_default_value=500
p12_description=Gene sets larger than this are excluded from the analysis
p12_fileFormat=
p12_flag=--max\=
p12_name=max.gene.set.size
p12_numValues=1..1
p12_optional=
p12_prefix=--max\=
p12_prefix_when_specified=--max\=
p12_range=1+
p12_type=java.lang.Integer
p12_value=
p13_MODE=
p13_TYPE=Integer
p13_default_value=15
p13_description=Gene sets smaller than this are excluded from the analysis
p13_fileFormat=
p13_flag=--min\=
p13_name=min.gene.set.size
p13_numValues=1..1
p13_optional=
p13_prefix=--min\=
p13_prefix_when_specified=--min\=
p13_range=1+
p13_type=java.lang.Integer
p13_value=
p14_MODE=
p14_TYPE=TEXT
p14_default_value=timestamp
p14_description=Numerical seed used to initiate the random permutation matrix.
p14_fileFormat=
p14_flag=--seed\=
p14_name=seed.for.permutation
p14_numValues=1..1
p14_optional=
p14_prefix=--seed\=
p14_prefix_when_specified=--seed\=
p14_type=java.lang.String
p14_value=
p15_MODE=
p15_TYPE=TEXT
p15_default_value=False
p15_description=GSEA will check the length of the input dataset to ensure a reasonable number of genes are included.
p15_fileFormat=
p15_flag=--ogllv\=
p15_name=override.gene.list.length.validation
p15_numValues=1..1
p15_optional=
p15_prefix=--ogllv\=
p15_prefix_when_specified=--ogllv\=
p15_type=java.lang.String
p15_value=True\=True;False\=False
p16_MODE=
p16_TYPE=Integer
p16_default_value=20
p16_description=Number of top gene sets to produce enrichment plots for.
p16_fileFormat=
p16_flag=--nplot\=
p16_name=plot.graphs
p16_numValues=0..1
p16_optional=
p16_prefix=--nplot\=
p16_prefix_when_specified=--nplot\=
p16_range=0+
p16_type=java.lang.Integer
p16_value=
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Input expression dataset in gct or tsv format
p1_fileFormat=gct;tsv
p1_flag=--dataset\=
p1_name=expression.dataset
p1_numValues=1..1
p1_optional=
p1_prefix=--dataset\=
p1_prefix_when_specified=--dataset\=
p1_type=java.io.File
p1_value=
p2_MODE=IN
p2_TYPE=FILE
p2_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/gene_sets/
p2_choiceDirFilter=*2023.1.*.symbols.gmt
p2_default_value=
p2_description=Gene sets database from GSEA website. Upload a gene set if your gene set is not listed as a choice from MSigDB.
p2_fileFormat=gmt;gmx;json
p2_flag=--gsdb\=
p2_name=gene.sets.database
p2_numValues=1+
p2_optional=
p2_prefix=--gsdb\=
p2_prefix_when_specified=--gsdb\=
p2_type=java.io.File
p2_value=
p3_MODE=
p3_TYPE=Integer
p3_default_value=1000
p3_description=Number of permutations to perform
p3_fileFormat=
p3_flag=--nperm\=
p3_name=number.of.permutations
p3_numValues=1..1
p3_optional=
p3_prefix=--nperm\=
p3_prefix_when_specified=--nperm\=
p3_range=0+
p3_type=java.lang.Integer
p3_value=
p4_MODE=IN
p4_TYPE=FILE
p4_default_value=
p4_description=Cls file - .cls
p4_fileFormat=cls
p4_flag=--cls\=
p4_name=phenotype.labels
p4_numValues=1..1
p4_optional=
p4_prefix=--cls\=
p4_prefix_when_specified=--cls\=
p4_type=java.io.File
p4_value=
p5_MODE=
p5_TYPE=TEXT
p5_default_value=False
p5_description=By default GSEA computes differential expression internally for the first phenotype in the cls vs. the second. Setting "reverse.phenotypes" to "True" computes for the second phenotype vs. the first.\nThis will have no effect on "numeric" format CLS files.
p5_fileFormat=
p5_flag=--reverse\=
p5_name=reverse.phenotypes
p5_numValues=1..1
p5_optional=
p5_prefix=--reverse\=
p5_prefix_when_specified=--reverse\=
p5_type=java.lang.String
p5_value=False\=False;True\=True
p6_MODE=
p6_TYPE=TEXT
p6_default_value=sample
p6_description=Type of permutations to perform
p6_fileFormat=
p6_flag=--perm\=
p6_name=permutation.type
p6_numValues=1..1
p6_optional=
p6_prefix=--perm\=
p6_prefix_when_specified=--perm\=
p6_type=java.lang.String
p6_value=sample\=phenotype;set\=gene_set
p7_MODE=
p7_TYPE=TEXT
p7_default_value=none
p7_description=Select a mathematical option to collapse a dataset from Gene IDs or Microarray probe IDs to Gene Symbols as used in MSigDB. For Human RNA-seq datasets, "Sum_of_probes" is recommended. For most other cases "Max_probe" should be used. If an option other than "none" is selected, a CHIP file containing the ID to symbol mappings must be provided to the "chip platform file" parameter.
p7_fileFormat=
p7_flag=--collapse\=
p7_name=collapse.dataset
p7_numValues=1..1
p7_optional=
p7_prefix=--collapse\=
p7_prefix_when_specified=--collapse\=
p7_type=java.lang.String
p7_value=none\=none;max\=Max_probe;sum\=Sum_of_probes;mean\=Mean_of_probes;median\=Median_of_probes;absmax\=Abs_max_of_probes
p8_MODE=IN
p8_TYPE=FILE
p8_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/annotations_versioned/
p8_choiceDirFilter=*2023.1.*.chip
p8_default_value=
p8_description=A Gene ID annotation file from GSEA website. Upload your own chip file if the one corresponding to your platform is not listed in the drop-down menu. A chip file is only required if collapse dataset is set to something other than "none".
p8_fileFormat=
p8_flag=--chip\=
p8_name=chip.platform.file
p8_numValues=0..1
p8_optional=on
p8_prefix=--chip\=
p8_prefix_when_specified=--chip\=
p8_type=java.io.File
p8_value=
p9_MODE=
p9_TYPE=TEXT
p9_default_value=signal-to-noise-ratio
p9_description=Class separation metric - gene markers are ranked using this metric to produce the gene list.
p9_fileFormat=
p9_flag=--metric\=
p9_name=metric.for.ranking.genes
p9_numValues=1..1
p9_optional=
p9_prefix=--metric\=
p9_prefix_when_specified=--metric\=
p9_type=java.lang.String
p9_value=signal-to-noise-ratio\=signal_to_noise_ratio;pearson-correlation\=pearson_correlation;information-correlation\=information_correlation;cosine-distance\=cosine_distance;median-difference\=median_difference;mean-difference\=mean_difference
privacy=public
quality=preproduction
src.repo=https\://github.com/genepattern/GSEA2
taskDoc=
taskType=
userid=acastanza
version=Update for 0.17.3 Core Changes