#CreateSignature
#Wed Nov 02 14:23:30 GMT-05:00 2011
JVMLevel=
LSID=urn\:lsid\:8080.root.cagt.igsp.duke.edu\:genepatternmodules\:3\:27
author=Mike West, Quanli Wang, Bill Barry, Jeffrey Chang
commandLine=/usr/local/bin/python /opt/SIGNATURE/pybinreg.py -v <version> --python\=/usr/local/bin/python --dwd_path\=/opt/SIGNATURE/BatchAdjust --binreg\=/opt/SIGNATURE/BinReg2.0 --matlab\=/usr/local/bin/matlab --arrayplot\=/opt/SIGNATURE/arrayplot.py --povray\=/usr/local/bin/povray --cluster\=/usr/local/bin/cluster --libpath\=/opt/SIGNATURE -z -g <num_genes> -m <num_metagenes> -l <log_the_data> --label_samples <label_samples> --draw_error_bars <draw_error_bars> <apply_dwd_normalization> <apply_quantile_normalization> <apply_shiftscale_normalization> <apply_dwd_bild_normalization> <normalization_reference> --burnin\=<burnin> --samples\=<niter> --skips\=<skips> --credible_interval\=<ci> <train0> <train1> <test>
cpuType=any
description=Binary regression.
fileFormat=
language=any
name=CreateSignature
os=any
p10_default_value=
p10_description=Apply DWD (Bild Method) normalization.
p10_fileFormat=
p10_name=apply_dwd_bild_normalization
p10_optional=on
p10_prefix_when_specified=
p10_type=java.lang.String
p10_value=--dwd_bild\=Yes;\=No
p11_MODE=IN
p11_TYPE=FILE
p11_default_value=
p11_description=Samples used as a reference for normalization. PCL, CDT, GCT, RES, ODF format.
p11_fileFormat=cdf;gct;gct,res,odf;pcl;res
p11_name=normalization_reference
p11_optional=on
p11_prefix_when_specified=--normalization_reference_file=
p11_type=java.io.File
p11_value=
p12_default_value=auto
p12_description=Apply log_2 to the data.
p12_fileFormat=
p12_name=log_the_data
p12_optional=
p12_prefix_when_specified=
p12_type=java.lang.String
p12_value=auto\=auto;yes\=yes;no\=no
p13_default_value=1000
p13_description=Number of burn-in samples.
p13_fileFormat=
p13_name=burnin
p13_optional=
p13_prefix_when_specified=
p13_type=java.lang.Integer
p13_value=
p14_default_value=5000
p14_description=Number of samples.
p14_fileFormat=
p14_name=niter
p14_optional=
p14_prefix_when_specified=
p14_type=java.lang.Integer
p14_value=
p15_default_value=1
p15_description=Number of skips.
p15_fileFormat=
p15_name=skips
p15_optional=
p15_prefix_when_specified=
p15_type=java.lang.Integer
p15_value=
p16_default_value=auto
p16_description=Label the samples in the scatter plot.
p16_fileFormat=
p16_name=label_samples
p16_optional=
p16_prefix_when_specified=
p16_type=java.lang.String
p16_value=auto\=auto;yes\=yes;no\=no
p17_default_value=auto
p17_description=Draw the error bars in the scatter plot.
p17_fileFormat=
p17_name=draw_error_bars
p17_optional=
p17_prefix_when_specified=
p17_type=java.lang.String
p17_value=auto\=auto;yes\=yes;no\=no
p18_default_value=95
p18_description=Credible interval.
p18_fileFormat=
p18_name=ci
p18_optional=
p18_prefix_when_specified=
p18_type=java.lang.Integer
p18_value=
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=File containing negative training samples (e.g. control samples). PCL, CDT, GCT, RES, ODF format.
p1_fileFormat=cdf;gct;gct,res,odf;pcl;res
p1_name=train0
p1_optional=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=IN
p2_TYPE=FILE
p2_default_value=
p2_description=File containing positive training samples (e.g. pathway activated samples). PCL, CDT, GCT, RES, ODF format.
p2_fileFormat=cdt;gct;gct,res,odf;pcl;res
p2_name=train1
p2_optional=
p2_prefix_when_specified=
p2_type=java.io.File
p2_value=
p3_MODE=IN
p3_TYPE=FILE
p3_default_value=
p3_description=File containing samples to predict. PCL, CDT, GCT, RES, ODF format.
p3_fileFormat=cdt;gct;gct,res,odf;pcl;res
p3_name=test
p3_optional=on
p3_prefix_when_specified=
p3_type=java.io.File
p3_value=
p4_default_value=2
p4_description=Version of Binreg algorithm.
p4_fileFormat=
p4_name=version
p4_optional=
p4_prefix_when_specified=
p4_type=java.lang.String
p4_value=1\=1;2\=2
p5_default_value=100
p5_description=Number of genes to use (usually from 50-500).
p5_fileFormat=
p5_name=num_genes
p5_optional=
p5_prefix_when_specified=
p5_type=java.lang.Integer
p5_value=
p6_default_value=2
p6_description=Number of metagenes to use (usually from 1-5).
p6_fileFormat=
p6_name=num_metagenes
p6_optional=
p6_prefix_when_specified=
p6_type=java.lang.Integer
p6_value=
p7_default_value=-q
p7_description=Apply quantile normalization.
p7_fileFormat=
p7_name=apply_quantile_normalization
p7_optional=on
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=-q\=Yes;\=No
p8_default_value=-s
p8_description=Apply shift-scale normalization.
p8_fileFormat=
p8_name=apply_shiftscale_normalization
p8_optional=on
p8_prefix_when_specified=
p8_type=java.lang.String
p8_value=-s\=Yes;\=No
p9_default_value=
p9_description=Apply DWD normalization.
p9_fileFormat=
p9_name=apply_dwd_normalization
p9_optional=on
p9_prefix_when_specified=
p9_type=java.lang.String
p9_value=-d\=Yes;\=No
pipelineModel=
privacy=public
quality=development
requiredPatchLSIDs=
requiredPatchURLs=
serializedModel=
taskType=SIGNATURE
userid=
version=
