manifest

#MAGeCK.Test
#Fri Mar 24 17:07:49 PDT 2017
JVMLevel=
LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00365\:0.0.2
author=Clarence Mah;Mesirov Lab
categories=CRISPR
commandLine=<run-with-env> -u mageck/0.5.5 mageck test <count.table> <control.ID> <gene.test.FDR.threshold> <keep.intermediate.files>  <normalization.method> <control.sgRNA> <treatment.id> <variance.from.all.samples> <sort.criteria> <remove.zero> <gene.log-fold.change.method> <output.prefix>  <normcounts.to.file> <p-value.adjustment.method>
cpuType=any
description=This subcommand tests and ranks sgRNAs and genes based on the read count tables provided.
fileFormat=
language=C
name=MAGeCK.Test
os=any
p11_MODE=
p11_TYPE=TEXT
p11_default_value=median
p11_description=Method to calculate gene log fold changes (LFC) from sgRNA LFCs. Available methods include the median/mean of all sgRNAs (median/mean), or the median/mean sgRNA that are ranked in front of the alpha cutoff in RRA (alphamedian/alphamean), or the sgRNA that has the second strongest LFC (secondbest). In the alphamedian/alphamean case, the number of sgRNAs correspond to the "goodsgrna" column in the output, and the gene LFC will be set to 0 if no sgRNA is in front of the alpha cutoff. Default median.
p10_fileFormat=
p10_flag=--gene-lfc-method 
p10_name=gene.log-fold.change.method
p10_numValues=0..1
p10_optional=on
p10_prefix=--gene-lfc-method 
p10_prefix_when_specified=--gene-lfc-method 
p10_type=java.lang.String
p10_value=median\=median;alphamedian\=alphamedian;mean\=mean;alphamean\=alphamean;secondbest\=secondbest
p11_MODE=
p11_TYPE=TEXT
p11_default_value=sample1
p11_description=The prefix of the output file(s). Default sample1.
p11_fileFormat=
p11_flag=-n
p11_name=output.prefix
p11_numValues=0..1
p11_optional=on
p11_prefix=-n 
p11_prefix_when_specified=-n 
p11_type=java.lang.String
p11_value=
p12_MODE=IN
p12_TYPE=FILE
p12_default_value=
p12_description=A list of control sgRNAs for normalization and for generating the null distribution of RRA.
p12_fileFormat=
p12_flag=--control-sgrna 
p12_name=control.sgRNA
p12_numValues=0..1
p12_optional=on
p12_prefix=--control-sgrna 
p12_prefix_when_specified=--control-sgrna 
p12_type=java.io.File
p12_value=
p13_MODE=
p13_TYPE=TEXT
p13_default_value=
p13_description=Write normalized read counts to file ([output-prefix].normalized.txt).
p13_fileFormat=
p13_flag=
p13_name=normcounts.to.file
p13_numValues=0..1
p13_optional=on
p13_prefix=
p13_prefix_when_specified=
p13_type=java.lang.String
p13_value=\=No;--normcounts-to-file\=Yes
p14_MODE=
p14_TYPE=TEXT
p14_default_value=
p14_description=Keep intermediate files.
p14_fileFormat=
p14_flag=
p14_name=keep.intermediate.files
p14_numValues=0..1
p14_optional=on
p14_prefix=
p14_prefix_when_specified=
p14_type=java.lang.String
p14_value=\=False;--keep-tmp\=True
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Provide a tab-separated count table. Each line in the table should include sgRNA name (1st column), targeting gene (2nd column) and read counts in each sample. A header line is optional.
p1_fileFormat=tsv;txt
p1_flag=-k
p1_name=count.table
p1_numValues=1..1
p1_optional=
p1_prefix=-k 
p1_prefix_when_specified=-k 
p1_type=java.io.File
p1_value=
p2_MODE=
p2_TYPE=TEXT
p2_default_value=
p2_description=Sample label or sample index (0 as the first sample) in the count table as treatment experiments, separated by comma (,). If sample label is provided, the labels must match the labels in the first line of the count table; for example, "HL60.final,KBM7.final". For sample index, "0,2" means the 1st and 3rd samples are treatment experiments.
p2_fileFormat=
p2_flag=--treatment-id 
p2_name=treatment.id
p2_numValues=1..1
p2_optional=
p2_prefix=--treatment-id 
p2_prefix_when_specified=--treatment-id 
p2_type=java.lang.String
p2_value=
p3_MODE=
p3_TYPE=TEXT
p3_default_value=
p3_description=Sample label or sample index in the count table as control experiments, separated by comma (,). Default is all the samples not specified in treatment experiments.
p3_fileFormat=
p3_flag=-c 
p3_name=control.ID
p3_numValues=0..1
p3_optional=on
p3_prefix=-c 
p3_prefix_when_specified=-c 
p3_type=java.lang.String
p3_value=
p4_MODE=
p4_TYPE=TEXT
p4_default_value=none
p4_description=Method for normalization, including "none" (no normalization), "median" (median normalization, default), "total" (normalization by total read counts), "control" (normalization by control sgRNAs specified by the --control-sgrna option).
p4_fileFormat=
p4_flag=--norm-method 
p4_name=normalization.method
p4_numValues=1..1
p4_optional=
p4_prefix=--norm-method 
p4_prefix_when_specified=--norm-method 
p4_type=java.lang.String
p4_value=none\=none;median\=median;total\=total;control\=control
p5_MODE=
p5_TYPE=TEXT
p5_default_value=0.25
p5_description=FDR threshold for gene test, default 0.25.
p5_fileFormat=
p5_flag=--gene-test-fdr-threshold 
p5_name=gene.test.FDR.threshold
p5_numValues=1..1
p5_optional=
p5_prefix=--gene-test-fdr-threshold 
p5_prefix_when_specified=--gene-test-fdr-threshold 
p5_type=java.lang.String
p5_value=
p6_MODE=
p6_TYPE=TEXT
p6_default_value=fdr
p6_description=Method for sgrna-level p-value adjustment, including false discovery rate (fdr), holm's method (holm), or pounds's method (pounds).
p6_fileFormat=
p6_flag=--adjust-method 
p6_name=p-value.adjustment.method
p6_numValues=0..1
p6_optional=
p6_prefix=--adjust-method 
p6_prefix_when_specified=--adjust-method 
p6_type=java.lang.String
p6_value=fdr\=fdr;holm\=holm;pounds\=pounds
p7_MODE=
p7_TYPE=TEXT
p7_default_value=
p7_description=Estimate the variance from all samples, instead of from only control samples. Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples.
p7_fileFormat=
p7_flag=
p7_name=variance.from.all.samples
p7_numValues=0..1
p7_optional=on
p7_prefix=
p7_prefix_when_specified=
p7_type=java.lang.String
p7_value=\=No;--variance-from-all-samples\=Yes
p8_MODE=
p8_TYPE=TEXT
p8_default_value=neg
p8_description=Sorting criteria, either by negative selection (neg) or positive selection (pos). Default negative selection.
p8_fileFormat=
p8_flag=--sort-criteria 
p8_name=sort.criteria
p8_numValues=0..1
p8_optional=on
p8_prefix=--sort-criteria 
p8_prefix_when_specified=--sort-criteria 
p8_type=java.lang.String
p8_value=neg\=Negative;pos\=Positive
p9_MODE=
p9_TYPE=TEXT
p9_default_value=none
p9_description=Whether to remove zero-count sgRNAs in control and/or treatment experiments. Default\: none (do not remove those zero-count sgRNAs).
p9_fileFormat=
p9_flag=--remove-zero 
p9_name=remove.zero
p9_numValues=0..1
p9_optional=on
p9_prefix=--remove-zero 
p9_prefix_when_specified=--remove-zero 
p9_type=java.lang.String
p9_value=none\=none;control\=control;treatment\=treatment;both\=both
privacy=private
quality=development
taskDoc=doc.pdf
taskType=CRISPR
userid=ckmah@ucsd.edu
version=