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Updated manifest, docs, etc ahead of the GSEA 4.2.0 release
Will be bumping the version to 20.3.x.
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,18 +1,18 @@ | ||
| #Fri, 05 Oct 2018 04:51:00 +0900 | ||
| # Copyright (c) 2003-2020 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| # Copyright (c) 2003-2021 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
| #GSEA | ||
| JVMLevel=11 | ||
| LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072\:999999999 | ||
| author=Aravind Subramanian, Pablo Tamayo, David Eby; Broad Institute | ||
| commandLine=/opt/gsea/GSEA_4.1.0/gsea-cli.sh GSEA -res <expression.dataset> -cls <phenotype.labels> -collapse <collapse.dataset> -mode <collapsing.mode.for.probe.sets.with.more.than.one.match> -norm <normalization.mode> -nperm <number.of.permutations> -permute <permutation.type> -rnd_type <randomization.mode> -scoring_scheme <scoring.scheme> -metric <metric.for.ranking.genes> -sort <gene.list.sorting.mode> -order <gene.list.ordering.mode> -include_only_symbols <omit.features.with.no.symbol.match> -make_sets <make.detailed.gene.set.report> -median <median.for.class.metrics> -num <number.of.markers> -plot_top_x <plot.graphs.for.the.top.sets.of.each.phenotype> -rnd_seed <random.seed> -save_rnd_lists <save.random.ranked.lists> -set_max <max.gene.set.size> -set_min <min.gene.set.size> <chip.platform.file> -gmx_list <gene.sets.database> -create_svgs <create.svgs> -create_gcts <create.gcts> -target_profile <target.profile> <selected.gene.sets> <output.file.name> <alt.delim> -dev_mode <dev.mode> -zip_report <create.zip> -run_as_genepattern true | ||
| commandLine=/opt/gsea/GSEA_4.2.0/gsea-cli.sh GSEA -res <expression.dataset> -cls <phenotype.labels> -collapse <collapse.dataset> -mode <collapsing.mode.for.probe.sets.with.more.than.one.match> -norm <normalization.mode> -nperm <number.of.permutations> -permute <permutation.type> -rnd_type <randomization.mode> -scoring_scheme <scoring.scheme> -metric <metric.for.ranking.genes> -sort <gene.list.sorting.mode> -order <gene.list.ordering.mode> -include_only_symbols <omit.features.with.no.symbol.match> -make_sets <make.detailed.gene.set.report> -median <median.for.class.metrics> -num <number.of.markers> -plot_top_x <plot.graphs.for.the.top.sets.of.each.phenotype> -rnd_seed <random.seed> -save_rnd_lists <save.random.ranked.lists> -set_max <max.gene.set.size> -set_min <min.gene.set.size> <chip.platform.file> -gmx_list <gene.sets.database> -create_svgs <create.svgs> -create_gcts <create.gcts> -target_profile <target.profile> <selected.gene.sets> <output.file.name> <alt.delim> -dev_mode <dev.mode> -zip_report true -run_as_genepattern true | ||
| cpuType=any | ||
| taskDoc=doc.html | ||
| description=Gene Set Enrichment Analysis. <strong>If you are using GSEA on RNA-seq data, please read <a href="http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA" target="_blank">these guidelines</a>.</strong> | ||
| fileFormat=zip | ||
| language=Java | ||
| name=GSEA | ||
| os=any | ||
| job.docker.image=genepattern/gsea_4.1.0\:0.1 | ||
| job.docker.image=genepattern/gsea_4.2.0\:0.1 | ||
|
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| p1_MODE=IN | ||
|
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@@ -359,7 +359,7 @@ p26_value= | |
| p27_MODE= | ||
| p27_TYPE=TEXT | ||
| p27_default_value=<expression.dataset_basename>.zip | ||
| p27_description=Name of the output file. Note that this only applies if create.zip\=true. | ||
| p27_description=Name of the output ZIP file. | ||
| p27_fileFormat= | ||
| p27_flag= | ||
| p27_name=output.file.name | ||
|
|
@@ -384,11 +384,11 @@ p28_value= | |
|
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| p29_MODE= | ||
| p29_TYPE=TEXT | ||
| p29_default_value=true | ||
| p29_description=Create a ZIP bundle of the output files. | ||
| p29_default_value=false | ||
| p29_description=Whether to save the dataset subsets backing the GSEA report heatmaps as GCT files; these will be subsets of your original dataset corresponding only to the genes of the heatmap. | ||
| p29_fileFormat= | ||
| p29_flag= | ||
| p29_name=create.zip | ||
| p29_name=create.gcts | ||
| p29_optional= | ||
| p29_prefix= | ||
| p29_prefix_when_specified= | ||
|
|
@@ -398,29 +398,16 @@ p29_value=false;true | |
| p30_MODE= | ||
| p30_TYPE=TEXT | ||
| p30_default_value=false | ||
| p30_description=Whether to save the dataset subsets backing the GSEA report heatmaps as GCT files; these will be subsets of your original dataset corresponding only to the genes of the heatmap. | ||
| p30_description=Enable developer mode. | ||
| p30_fileFormat= | ||
| p30_flag= | ||
| p30_name=create.gcts | ||
| p30_name=dev.mode | ||
| p30_optional= | ||
| p30_prefix= | ||
| p30_prefix_when_specified= | ||
| p30_type=java.lang.String | ||
| p30_value=false;true | ||
|
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||
| p31_MODE= | ||
| p31_TYPE=TEXT | ||
| p31_default_value=false | ||
| p31_description=Enable developer mode. | ||
| p31_fileFormat= | ||
| p31_flag= | ||
| p31_name=dev.mode | ||
| p31_optional= | ||
| p31_prefix= | ||
| p31_prefix_when_specified= | ||
| p31_type=java.lang.String | ||
| p31_value=false;true | ||
|
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| pipelineModel= | ||
| privacy=public | ||
| quality=development | ||
|
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@@ -430,6 +417,6 @@ serializedModel= | |
| taskType=Pathway Analysis | ||
| categories=gsea;pathway analysis | ||
| [email protected] | ||
| version=Fixed minor typo. | ||
| version=Updated with the GSEA Desktop 4.2.0 code base with numerous bug fixes. Fixed some issues handling datasets with missing values. Introduced the Spearman metric. Fixed issue with the min-sample check with gene_set permutation mode. Changed the FDR q-value scale on the NES vs Significance plot. | ||
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| publicationDate=10/05/2018 04\:51 | ||
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| [{name: "Basic parameters", description: "These parameters are essential for the analysis.", parameters: ["expression.dataset", "gene.sets.database", "number.of.permutations", "phenotype.labels", "target.profile", "permutation.type", "collapse.dataset", "chip.platform.file", "output.file.name" ]}, | ||
| {name: "Advanced parameters", description: "Additional parameters with standard defaults; typically you will run GSEA with these parameters set to their default values.", hidden: false}, | ||
| {name: "Advanced parameters/Algorithmic", hidden: true, parameters: ["scoring.scheme", "metric.for.ranking.genes", "gene.list.sorting.mode", "gene.list.ordering.mode", "max.gene.set.size", "min.gene.set.size", "collapsing.mode.for.probe.sets.with.more.than.one.match", "normalization.mode", "randomization.mode", "omit.features.with.no.symbol.match", "median.for.class.metrics", "number.of.markers", "random.seed", "save.random.ranked.lists", "selected.gene.sets", "dev.mode", "alt.delim"]}, | ||
| {name: "Advanced parameters/Reporting", hidden: true, parameters: ["plot.graphs.for.the.top.sets.of.each.phenotype", "make.detailed.gene.set.report", "create.svgs", "create.gcts", "create.zip"]} | ||
| {name: "Advanced parameters/Reporting", hidden: true, parameters: ["plot.graphs.for.the.top.sets.of.each.phenotype", "make.detailed.gene.set.report", "create.svgs", "create.gcts"]} | ||
| ] |
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| @@ -1,5 +1,5 @@ | ||
| #Thu, 22 Apr 2021 11:20:36 -0700 | ||
| LSID.noVersion=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00072 | ||
| release.version=20.2 | ||
| build.number=4 | ||
| release.version=20.3 | ||
| build.number=-1 | ||
| build.timestamp=Thu, 22 Apr 2021 11\:20\:36 -0700 |