manifest

#Thu, 09 Feb 2023 01:07:58 -0400
JVMLevel=
LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00125\:6.12
author=Jen Dobson, Rameen Beroukhim, Gad Getz
commandLine=<run-with-env> -u matlab-mcr/2014a <libdir>gp_gistic2_from_seg -b . -seg <seg.file> <markers.file> <maxspace> -alf <array.list.file> -cnv <cnv.file> -refgene <refgene.file> -ta <amplifications.threshold> -td <deletions.threshold> -js <join.segment.size> -qvt <q-value.threshold> -rx <remove.X> -cap <cap.val> -conf <confidence.level> -genegistic <gene.gistic> -broad <run.broad.analysis> -brlen <focal.length.cutoff> -maxseg <max.sample.segs> -armpeel <arm.peel> -scent <sample.center> -gcm <gene.collapse.method> -arb 1 -peak_type robust -fname <output.prefix> -genepattern 1 -twosides 0 -saveseg 0 -savedata 0 -smalldisk 0 -smallmem 1 -savegene 1 -v 0 <logdat>
cpuType=any
description=Genomic Identification of Significant Targets in Cancer (version 2.0.23)
fileFormat=png;v2.pdf;gistic.txt;seg.txt
language=MATLAB
name=GISTIC_2.0
os=linux

p1_MODE=IN
p1_TYPE=FILE
p1_choiceDir=https://datasets.genepattern.org/gpftp/module_support_files/GISTIC/index_directory.json
p1_choiceDirFilter=*.mat
p1_choiceAllowCustom=false
p1_default_value=
p1_description=The reference genome file input provides cytoband and gene location information.
p1_fileFormat=mat
p1_flag=
p1_name=refgene.file
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=

p2_MODE=IN
p2_TYPE=FILE
p2_default_value=
p2_description=The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.
p2_fileFormat=glad;seg;txt
p2_flag=
p2_name=seg.file
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.io.File
p2_value=

p3_MODE=IN
p3_TYPE=FILE
p3_default_value=
p3_description=The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. If not already, markers are sorted by genomic position.
p3_fileFormat=cn;txt
p3_flag=
p3_name=markers.file
p3_optional=on
p3_prefix=
p3_prefix_when_specified=-mk 
p3_type=java.io.File
p3_value=

p4_MODE=
p4_TYPE=TEXT
p4_default_value=10000
p4_description=Set maxspace to generate pseudo-markers instead of creating a markers file. The param defines the maximum allowed spacing between pseudo-markers, in bases. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number. When 'markers file' is set 'maxspace' is ignored. When neither are set, generate pseudo-markers, with maxspace=10,000.
p4_fileFormat=
p4_flag=-maxspace 
p4_name=maxspace
p4_numValues=0..1
p4_optional=on
p4_prefix=-maxspace 
p4_prefix_when_specified=-maxspace 
p4_type=java.lang.String
p4_value=

p5_MODE=IN
p5_TYPE=FILE
p5_default_value=
p5_description=The array list file is an optional file identifying the subset of samples to be used in the analysis. It is a one column file with an optional header. The sample identifiers listed in the array list file must match the sample names given in the segmentation file.
p5_fileFormat=alf;txt
p5_flag=
p5_name=array.list.file
p5_optional=on
p5_prefix=
p5_prefix_when_specified=
p5_type=java.io.File
p5_value=

p6_MODE=IN
p6_TYPE=FILE
p6_default_value=
p6_description=Specifies germline CNV (or other highly variant) regions to exclude from significance analysis. There are two forms for the cnv file\: one allows CNVs to be identified by marker names in a single column; the other identifies excluded regions using their genomic location.
p6_fileFormat=CNV
p6_flag=
p6_name=cnv.file
p6_optional=on
p6_prefix=
p6_prefix_when_specified=
p6_type=java.io.File
p6_value=

p7_MODE=
p7_TYPE=TEXT
p7_default_value=1
p7_description=Flag indicating that the gene GISTIC algorithm should be used to calculate the significant regions of deletion using gene locations instead of a marker locations.
p7_fileFormat=
p7_flag=
p7_name=gene.gistic
p7_optional=
p7_prefix=
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=1\=yes;0\=no

p8_MODE=
p8_TYPE=TEXT
p8_default_value=0.1
p8_description=Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
p8_fileFormat=
p8_flag=
p8_name=amplifications.threshold
p8_optional=
p8_prefix=
p8_prefix_when_specified=
p8_type=java.lang.String
p8_value=

p9_MODE=
p9_TYPE=TEXT
p9_default_value=0.1
p9_description=Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
p9_fileFormat=
p9_flag=
p9_name=deletions.threshold
p9_optional=
p9_prefix=
p9_prefix_when_specified=
p9_type=java.lang.String
p9_value=

p10_MODE=
p10_TYPE=TEXT
p10_default_value=4
p10_description=Smallest number of markers to allow in segments from the segmented data. Segments that contain a number of markers less than or equal to this number are joined to the neighboring segment that is closest in copy number.
p10_fileFormat=
p10_flag=
p10_name=join.segment.size
p10_optional=
p10_prefix=
p10_prefix_when_specified=
p10_type=java.lang.String
p10_value=

p11_MODE=
p11_TYPE=TEXT
p11_default_value=0.25
p11_description=Maximum false discovery rate for a region to be considered significant.
p11_fileFormat=
p11_flag=
p11_name=q-value.threshold
p11_optional=
p11_prefix=
p11_prefix_when_specified=
p11_type=java.lang.String
p11_value=

p12_MODE=
p12_TYPE=TEXT
p12_default_value=1
p12_description=Flag indicating whether to remove data from the X-chromosome before analysis.
p12_fileFormat=
p12_flag=
p12_name=remove.X
p12_optional=
p12_prefix=
p12_prefix_when_specified=
p12_type=java.lang.String
p12_value=1\=yes;0\=no

p13_MODE=
p13_TYPE=TEXT
p13_default_value=1.5
p13_description=Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap.
p13_fileFormat=
p13_flag=-cap 
p13_name=cap.val
p13_optional=
p13_prefix=
p13_prefix_when_specified=
p13_type=java.lang.String
p13_value=1.0\=1.0;1.5\=1.5;2.0\=2.0;2.5\=2.5;Inf\=Inf

p14_MODE=
p14_TYPE=TEXT
p14_default_value=0.90
p14_description=Confidence level used to calculate the region containing a driver.
p14_fileFormat=
p14_flag=
p14_name=confidence.level
p14_optional=
p14_prefix=
p14_prefix_when_specified=
p14_type=java.lang.String
p14_value=

p15_MODE=
p15_TYPE=TEXT
p15_default_value=0
p15_description=Flag indicating whether an additional broad-level analysis should be performed.
p15_fileFormat=
p15_flag=
p15_name=run.broad.analysis
p15_optional=
p15_prefix=
p15_prefix_when_specified=
p15_type=java.lang.String
p15_value=1\=yes;0\=no

p16_MODE=
p16_TYPE=TEXT
p16_default_value=0.50
p16_description=Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
p16_fileFormat=
p16_flag=
p16_name=focal.length.cutoff
p16_optional=
p16_prefix=
p16_prefix_when_specified=
p16_type=java.lang.String
p16_value=

p17_MODE=
p17_TYPE=TEXT
p17_default_value=2500
p17_description=Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
p17_fileFormat=
p17_flag=
p17_name=max.sample.segs
p17_optional=
p17_prefix=
p17_prefix_when_specified=
p17_type=java.lang.String
p17_value=

p18_MODE=
p18_TYPE=TEXT
p18_default_value=0
p18_description=Whether to perform arm level peel off. This helps separate peaks which cleans up noise.
p18_fileFormat=
p18_flag=
p18_name=arm.peel
p18_optional=
p18_prefix=
p18_prefix_when_specified=
p18_type=java.lang.String
p18_value=1\=yes;0\=no

p19_MODE=
p19_TYPE=TEXT
p19_default_value=median
p19_description=Method for centering each sample prior to the GISTIC analysis.
p19_fileFormat=
p19_flag=
p19_name=sample.center
p19_optional=
p19_prefix=
p19_prefix_when_specified=
p19_type=java.lang.String
p19_value=median;mean;none

p20_MODE=
p20_TYPE=TEXT
p20_default_value=extreme
p20_description=Method for reducing marker-level copy number data to the gene-level copy number data in the gene tables. Markers contained in the gene are used when available, otherwise the flanking marker or markers are used.
p20_fileFormat=
p20_flag=
p20_name=gene.collapse.method
p20_optional=
p20_prefix=
p20_prefix_when_specified=
p20_type=java.lang.String
p20_value=mean;median;min;max;extreme

p21_MODE=
p21_TYPE=TEXT
p21_default_value=<seg.file_basename>
p21_description=The prefix for the output file name
p21_fileFormat=
p21_flag=
p21_name=output.prefix
p21_optional=
p21_prefix=
p21_prefix_when_specified=
p21_type=java.lang.String
p21_value=

p22_MODE=
p22_TYPE=TEXT
# <actual>=<display>
p22_choices=\=autodetect;0=linear;1=log2
p22_default_value=
p22_description=The '-logdat' param to apply log2 ratio for SNP arrays, default=autodetect
p22_fileFormat=
p22_flag=
p22_name=logdat
p22_optional=on
p22_prefix=
p22_prefix_when_specified=-logdat 
p22_type=java.lang.String
p22_value=

pipelineModel=
privacy=public
quality=production
requiredPatchLSIDs=
requiredPatchURLs=
serializedModel=
taskDoc=doc.html
taskType=SNP Analysis
userid=GenePattern
version=Moved data from gpftp to datasets