manifest_ssGSEA2

#ssGSEA2
#Tue Jul 11 18:42:00 UTC 2023
JVMLevel=
LSID=urn\:lsid\:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal\:genepatternmodules\:590\:1.2.2
author=
commandLine=python3 <libdir>run.ssgsea2.py --libdir\=<libdir> <expression.dataset> <gene.sets.database> <collapse.dataset> <chip.platform.file> <enrichment.algorithm> <weighting.exponent> <max.gene.set.size> <min.gene.set.size> <override.gene.list.length.validation> <plot.graphs> --cpu\=<job.cpuCount>
cpuType=any
description=New ssGSEA (GSEA.jl 0.13.3)
documentationUrl=
fileFormat=
job.cpuCount=3
job.docker.image=acastanza/gsea2\:0.13.3
job.memory=
job.walltime=
language=any
name=ssGSEA2
os=any
p10_MODE=
p10_TYPE=Integer
p10_default_value=20
p10_description=Number of top gene sets to produce enrichment plots for.
p10_fileFormat=
p10_flag=--nplot\=
p10_name=plot.graphs
p10_numValues=0..1
p10_optional=
p10_prefix=--nplot\=
p10_prefix_when_specified=--nplot\=
p10_range=0+
p10_type=java.lang.Integer
p10_value=
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Input within-sample ranked dataset in gct or tsv format
p1_fileFormat=gct
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
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=TEXT
p3_default_value=none
p3_description=Select a mathematical option to collapse a dataset from Gene IDs or Microarray probe IDs to Gene Symbols as used in MSigDB. For Preranked datasets "absmax" is recommended. 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.
p3_fileFormat=
p3_flag=--collapse\=
p3_name=collapse.dataset
p3_numValues=1..1
p3_optional=
p3_prefix=--collapse\=
p3_prefix_when_specified=--collapse\=
p3_type=java.lang.String
p3_value=none\=none;max\=Max_probe;sum\=Sum_of_probes;mean\=Mean_of_probes;median\=Median_of_probes;absmax\=Abs_max_of_probes
p4_MODE=IN
p4_TYPE=FILE
p4_choiceDir=ftp\://ftp.broadinstitute.org/pub/gsea/annotations_versioned/
p4_choiceDirFilter=*2023.1.*.chip
p4_default_value=
p4_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".
p4_fileFormat=
p4_flag=--chip\=
p4_name=chip.platform.file
p4_numValues=0..1
p4_optional=on
p4_prefix=--chip\=
p4_prefix_when_specified=--chip\=
p4_type=java.io.File
p4_value=
p5_MODE=
p5_TYPE=TEXT
p5_default_value=ks
p5_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 the next-generation "kli, kliop, or kliom" GSEA methods.
p5_fileFormat=
p5_flag=--alg\=
p5_name=enrichment.algorithm
p5_numValues=1..1
p5_optional=
p5_prefix=--alg\=
p5_prefix_when_specified=--alg\=
p5_type=java.lang.String
p5_value=ks\=Kolmogorov-Smirnov (Classic GSEA);ksa\=Kolmogorov-Smirnov Area;kli\=KLI;kliop\=KLIIO;kliom\=KLIOM
p6_MODE=
p6_TYPE=Floating Point
p6_default_value=1
p6_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)
p6_fileFormat=
p6_flag=--exponent\=
p6_name=weighting.exponent
p6_numValues=1..1
p6_optional=
p6_prefix=--exponent\=
p6_prefix_when_specified=--exponent\=
p6_type=java.lang.Float
p6_value=
p7_MODE=
p7_TYPE=Integer
p7_default_value=500
p7_description=Gene sets larger than this are excluded from the analysis
p7_fileFormat=
p7_flag=--max\=
p7_name=max.gene.set.size
p7_numValues=1..1
p7_optional=
p7_prefix=--max\=
p7_prefix_when_specified=--max\=
p7_range=1+
p7_type=java.lang.Integer
p7_value=
p8_MODE=
p8_TYPE=Integer
p8_default_value=15
p8_description=Gene sets smaller than this are excluded from the analysis
p8_fileFormat=
p8_flag=--min\=
p8_name=min.gene.set.size
p8_numValues=1..1
p8_optional=
p8_prefix=--min\=
p8_prefix_when_specified=--min\=
p8_range=1+
p8_type=java.lang.Integer
p8_value=
p9_MODE=
p9_TYPE=TEXT
p9_default_value=False
p9_description=GSEA will check the length of the input dataset to ensure a reasonable number of genes are included.
p9_fileFormat=
p9_flag=--ogllv\=
p9_name=override.gene.list.length.validation
p9_numValues=1..1
p9_optional=
p9_prefix=--ogllv\=
p9_prefix_when_specified=--ogllv\=
p9_type=java.lang.String
p9_value=True\=True;False\=False
privacy=public
quality=development
src.repo=
taskDoc=
taskType=
userid=acastanza
version=GSEA.jl 0.13.3