Mercurial > repos > bgruening > diffbind
changeset 15:194e3f2c1d86 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
| author | iuc |
|---|---|
| date | Tue, 09 Jul 2019 18:46:09 -0400 |
| parents | c97a786e8fb5 |
| children | 163688bb8f73 |
| files | diffbind.R diffbind.xml |
| diffstat | 2 files changed, 8 insertions(+), 9 deletions(-) [+] |
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--- a/diffbind.R Thu Jun 07 05:21:22 2018 -0400 +++ b/diffbind.R Tue Jul 09 18:46:09 2019 -0400 @@ -57,16 +57,15 @@ bamReads=bams, bamControl=ctrls, Peaks=peaks, - Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot - stringsAsFactors=FALSE) + Tissue=samples) # using "Tissue" column to display ids as labels in PCA plot } else { + sampleTable <- data.frame(SampleID=samples, Replicate=samples, Condition=groups, bamReads=bams, Peaks=peaks, - Tissue=samples, - stringsAsFactors=FALSE) + Tissue=samples) } sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter) @@ -126,7 +125,7 @@ Strand=gsub("\\*", ".", strand(resSorted)), mcols(resSorted)) } -write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) +write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, row.names = FALSE) # Output binding affinity scores if (!is.null(opt$bmatrix)) {
--- a/diffbind.xml Thu Jun 07 05:21:22 2018 -0400 +++ b/diffbind.xml Tue Jul 09 18:46:09 2019 -0400 @@ -1,9 +1,9 @@ -<tool id="diffbind" name="DiffBind" version="2.6.6.4"> +<tool id="diffbind" name="DiffBind" version="2.10.0"> <description> differential binding analysis of ChIP-Seq peak data</description> <requirements> - <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> - <requirement type="package" version="1.20.0">r-getopt</requirement> - <requirement type="package" version="0.2.15">r-rjson</requirement> + <requirement type="package" version="2.10.0">bioconductor-diffbind</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="0.2.20">r-rjson</requirement> </requirements> <stdio> <regex match="Execution halted"