manifest

# Copyright (c) 2003-2022 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California.  All rights reserved.
#Chip2Chip
JVMLevel=11
LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00361\:999999999
author=Aravind Subramanian, Broad Institute
commandLine=/opt/gsea/GSEA_4.3.2/gsea-cli.sh Chip2Chip -gmx_list <gene.sets.database> -chip <chip.platform.file> -genesetmatrix_format <gene.set.matrix.output.format> -show_etiology <output.verbose.mapping.details> <alt.delim> <selected.gene.sets> -dev_mode <dev.mode> -zip_report <create.zip> -run_as_genepattern true
cpuType=any
taskDoc=doc.html
description=Chip2Chip conversion from the GSEA project
fileFormat=gmt;zip;txt;html;xls;css
language=Java
name=Chip2Chip
os=any
job.docker.image=genepattern/gsea_4.3.2\:0.1

p1_MODE=IN
p1_TYPE=FILE
p1_choiceDir=http://127.0.0.1:8092/gsea-public/gp_modules_gmt.json
p1_default_value=
p1_description=Gene sets database from GSEA website.
p1_fileFormat=gmt;gmx;grp
p1_numValues=1+
p1_flag=
p1_name=gene.sets.database
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=

p2_MODE=IN
p2_TYPE=FILE
p2_choiceDir=https://www.gsea-msigdb.org/gsea/msigdb/gp_modules_chip.json
p2_default_value=
p2_description=DNA Chip (array) annotation file from GSEA website.  Upload your own chip file if the one corresponding to your DNA Microarray platform is not listed in the drop-down menu.  A chip file is only required if collapse dataset is set to true.
p2_fileFormat=chip
p2_flag=
p2_name=chip.platform.file
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.io.File
p2_value=

p3_MODE=
p3_TYPE=TEXT
p3_default_value=gmt
p3_description=Output format for the gene set matrix.
p3_fileFormat=
p3_flag=
p3_name=gene.set.matrix.output.format
p3_optional=
p3_prefix=
p3_prefix_when_specified=
p3_type=java.lang.String
p3_value=gmt;gmx

p4_MODE=
p4_TYPE=TEXT
p4_default_value=true
p4_description=Show the etiology for the features.
p4_fileFormat=
p4_flag=
p4_name=output.verbose.mapping.details
p4_optional=
p4_prefix=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=false;true

p5_MODE=
p5_TYPE=TEXT
p5_default_value=
p5_description=Semicolon-separated list of gene sets from the provided gene sets database files (GMT/GMX/GRP).  If you are using multiple files then you *must* prefix each selected gene set with its file name followed by '#' (like "my_file1.gmt#selected_gene_set1,my_file2.gmt#selected_gene_set2").  With a single file only the names are necessary.  Leave this blank to select all gene sets.
p5_fileFormat=
p5_flag=
p5_name=selected.gene.sets
p5_optional=on
p5_prefix=
p5_prefix_when_specified=-selected_gene_sets 
p5_type=java.lang.String
p5_value=

p6_MODE=
p6_TYPE=TEXT
p6_default_value=
p6_description=Optional alternate delimiter character for gene set names instead of comma for use with selected.gene.sets.  If used, a semicolon is recommended.
p6_fileFormat=
p6_flag=
p6_name=alt.delim
p6_optional=on
p6_prefix=
p6_prefix_when_specified=--altDelim=
p6_type=java.lang.String
p6_value=

p7_MODE=
p7_TYPE=TEXT
p7_default_value=true
p7_description=Create a ZIP bundle of the output files.
p7_fileFormat=
p7_flag=
p7_name=create.zip
p7_optional=
p7_prefix=
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=false;true
p8_MODE=

p8_TYPE=TEXT
p8_default_value=false
p8_description=Enable developer mode.
p8_fileFormat=
p8_flag=
p8_name=dev.mode
p8_optional=
p8_prefix=
p8_prefix_when_specified=
p8_type=java.lang.String
p8_value=false;true

pipelineModel=
privacy=public
quality=development
requiredPatchLSIDs=
requiredPatchURLs=
serializedModel=
taskType=Gene List Selection
categories=beta;gsea
userid=eby@broadinstitute.org
version=Development revision with GSEA v4.3.x code.