Mercurial > repos > bgruening > diffbind
changeset 10:b1b96b6ed60c draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 16 Jan 2014 04:17:16 -0500 |
| parents | 20c431b4cf74 |
| children | a8dc71379df0 |
| files | diffbind.R diffbind.xml tool_dependencies.xml |
| diffstat | 3 files changed, 20 insertions(+), 13 deletions(-) [+] |
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--- a/diffbind.R Tue Jan 14 18:07:20 2014 -0500 +++ b/diffbind.R Thu Jan 16 04:17:16 2014 -0500 @@ -30,7 +30,6 @@ library('DiffBind') # used to save to BED, GFF or WIG format -library('rtracklayer') if ( !is.null(opt$plots) ) { pdf(opt$plots) @@ -39,12 +38,14 @@ sample = dba(sampleSheet=opt$infile, peakFormat='bed') sample_count = dba.count(sample) -sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION) +sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2) sample_analyze = dba.analyze(sample_contrast) diff_bind = dba.report(sample_analyze) - +orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE) -export(diff_bind, opt$outfile, format=opt$format) +resSorted <- diff_bind[order(diff_bind$FDR),] +write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE, col.names = FALSE) + dev.off() sessionInfo()
--- a/diffbind.xml Tue Jan 14 18:07:20 2014 -0500 +++ b/diffbind.xml Thu Jan 16 04:17:16 2014 -0500 @@ -7,14 +7,22 @@ <requirement type="package" version="1.0.17">deseq2</requirement> <requirement type="package" version="1.8.3">diffbind</requirement> </requirements> - <command interpreter="Rscript"> - diffbind.R + <command> + ## seems that diffbind also needs file extensions to work properly + #set $counter = 1 + #for $sample in $samples: + ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && + ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && + ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && + ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && + #set $counter = $counter + 1 + #end for + + Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R -i $infile -o $outfile -p $plots -f $format - ; - cat $infile; </command> <stdio> <regex match="Execution halted" @@ -53,8 +61,10 @@ <configfiles> <configfile name="infile"> SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks +#set $counter = 1 #for $sample in $samples: -$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks +$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks +#set $counter = $counter + 1 #end for </configfile> </configfiles>
--- a/tool_dependencies.xml Tue Jan 14 18:07:20 2014 -0500 +++ b/tool_dependencies.xml Thu Jan 16 04:17:16 2014 -0500 @@ -31,10 +31,6 @@ <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/zlibbioc_1.8.0.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/Rsamtools_1.14.2.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/DiffBind_1.8.3.tar.gz</package> - <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/XML_3.98-1.1.tar.gz</package> - <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/BSgenome_1.30.0.tar.gz</package> - <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/RCurl_1.95-4.1.tar.gz</package> - <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/rtracklayer_1.22.0.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/getopt_1.20.0.tar.gz</package> </action> </actions>