Mercurial > repos > bgruening > diffbind
changeset 9:20c431b4cf74 draft
Uploaded
author | bgruening |
---|---|
date | Tue, 14 Jan 2014 18:07:20 -0500 |
parents | 7929c8b3f6f9 |
children | b1b96b6ed60c |
files | diffbind.R diffbind.xml |
diffstat | 2 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/diffbind.R Tue Jan 14 08:13:24 2014 -0500 +++ b/diffbind.R Tue Jan 14 18:07:20 2014 -0500 @@ -23,8 +23,8 @@ # if help was asked for print a friendly message # and exit with a non-zero error code if ( !is.null(opt$help) ) { - cat(getopt(spec, usage=TRUE)); - q(status=1); + cat(getopt(spec, usage=TRUE)); + q(status=1); } @@ -33,11 +33,11 @@ library('rtracklayer') if ( !is.null(opt$plots) ) { - pdf(opt$plots) + pdf(opt$plots) } -sample = dba(sampleSheet=opt$infile) +sample = dba(sampleSheet=opt$infile, peakFormat='bed') sample_count = dba.count(sample) sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION) sample_analyze = dba.analyze(sample_contrast)
--- a/diffbind.xml Tue Jan 14 08:13:24 2014 -0500 +++ b/diffbind.xml Tue Jan 14 18:07:20 2014 -0500 @@ -13,6 +13,8 @@ -o $outfile -p $plots -f $format + ; + cat $infile; </command> <stdio> <regex match="Execution halted" @@ -49,12 +51,12 @@ </param> </inputs> <configfiles> - <configfile name="infile"> +<configfile name="infile"> SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks #for $sample in $samples: $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks #end for - </configfile> +</configfile> </configfiles> <outputs> <data format="bed" name="outfile" label="Differential binding sites on ${on_string}"> @@ -63,7 +65,7 @@ <when input="format" value="gff" format="gff" /> </change_format> </data> - <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> + <data format="pdf" name="plots" label="Differential binding sites on ${on_string}"> <filter>pdf == True</filter> </data> </outputs>