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# Copyright (c) 2003-2017 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved.
author=GenePattern
taskDoc=doc.html
description=Performs single sample GSEA Projection
commandLine=<R2.15_Rscript> <libdir>ssGSEAProjection.R -l<libdir> -i<input.gct.file> -o<output.file.prefix> -D<gene.sets.database.files> -c<gene.symbol.column> -s<gene.set.selection> -n<sample.normalization.method> -w<weighting.exponent> -v<min.gene.set.size> -C<combine.mode>
JVMLevel=
language=R
name=ssGSEAProjection
fileFormat=gct
privacy=public
userid=GenePattern
quality=production
taskType=Projection
version=Beta series: Unified the Gene Set DB selector parameters and better downloading of MSigDB files. Removed Java dependency.
cpuType=any
os=any
LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00270\:999999999
publicationDate=03/22/2012 11\:14
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Input gct file. This module does not allow missing values.
p1_fileFormat=gct
p1_name=input.gct.file
p1_optional=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_default_value=
p2_description=Output filename prefix. If unspecified, is set to <prefix of input.gct.file>.PROJ.
p2_fileFormat=
p2_name=output.file.prefix
p2_optional=on
p2_prefix_when_specified=
p2_type=java.lang.String
p2_value=
p3_MODE=IN
p3_TYPE=FILE
p3_default_value=
p3_description=Gene sets database from GSEA website. Upload a gene set if your gene set is not listed as a choice from MsigDB.
p3_fileFormat=gmt;gmx;grp
p3_numValues=1+
p3_flag=
p3_name=gene.sets.database.files
p3_optional=
p3_prefix=
p3_prefix_when_specified=
p3_type=java.io.File
p3_value=ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c1.all.v6.0.symbols.gmt\=c1.all.v6.0.symbols.gmt [Positional];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.all.v6.0.symbols.gmt\=c2.all.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cgp.v6.0.symbols.gmt\=c2.cgp.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.v6.0.symbols.gmt\=c2.cp.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.biocarta.v6.0.symbols.gmt\=c2.cp.biocarta.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.kegg.v6.0.symbols.gmt\=c2.cp.kegg.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c2.cp.reactome.v6.0.symbols.gmt\=c2.cp.reactome.v6.0.symbols.gmt [Curated];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.all.v6.0.symbols.gmt\=c3.all.v6.0.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.mir.v6.0.symbols.gmt\=c3.mir.v6.0.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c3.tft.v6.0.symbols.gmt\=c3.tft.v6.0.symbols.gmt [Motif];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.all.v6.0.symbols.gmt\=c4.all.v6.0.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cgn.v6.0.symbols.gmt\=c4.cgn.v6.0.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c4.cm.v6.0.symbols.gmt\=c4.cm.v6.0.symbols.gmt [Computational];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.all.v6.0.symbols.gmt\=c5.all.v6.0.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.bp.v6.0.symbols.gmt\=c5.bp.v6.0.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.cc.v6.0.symbols.gmt\=c5.cc.v6.0.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c5.mf.v6.0.symbols.gmt\=c5.mf.v6.0.symbols.gmt [Gene Ontology];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c6.all.v6.0.symbols.gmt\=c6.all.v6.0.symbols.gmt [Oncogenic Signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/c7.all.v6.0.symbols.gmt\=c7.all.v6.0.symbols.gmt [Immunologic signatures];ftp\://gpftp.broadinstitute.org/module_support_files/msigdb/gmt/h.all.v6.0.symbols.gmt\=h.all.v6.0.symbols.gmt [Hallmarks]
p4_default_value=Name
p4_description=Specifies the gct data column containing gene symbols. In most cases this will be "Column 1".
p4_fileFormat=
p4_name=gene.symbol.column
p4_optional=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=Name=\Column 1;Description\=Column 2
p5_default_value=ALL
p5_description=Comma-separated list of gene set names on which to project expression data. Set to "ALL" if projecting to all defined gene sets.
p5_fileFormat=
p5_name=gene.set.selection
p5_optional=
p5_prefix_when_specified=
p5_type=java.lang.String
p5_value=
p6_default_value=rank
p6_description=Method used to normalize gene expression data
p6_fileFormat=
p6_name=sample.normalization.method
p6_optional=
p6_prefix_when_specified=
p6_type=java.lang.String
p6_value=rank;log;log.rank
p7_default_value=0.75
p7_description=Module authors strongly recommend against changing from default.
p7_fileFormat=
p7_name=weighting.exponent
p7_optional=
p7_prefix_when_specified=
p7_type=java.lang.Float
p7_value=
p8_default_value=10
p8_description=Gene sets with overlap smaller than this are excluded from the analysis.
p8_fileFormat=
p8_name=min.gene.set.size
p8_optional=
p8_prefix_when_specified=
p8_type=java.lang.Integer
p8_value=
p9_default_value=combine.add
p9_description=Options for combining enrichment scores for paired *_UP and *_DN gene sets
p9_fileFormat=
p9_name=combine.mode
p9_optional=
p9_prefix=
p9_prefix_when_specified=
p9_type=java.lang.String
p9_value=combine.off;combine.replace;combine.add
p9_default_value=combine.add