Mercurial > repos > sblanck > smagexp
changeset 34:0a74b8de4c10 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f
| author | sblanck |
|---|---|
| date | Thu, 21 Jun 2018 10:41:50 -0400 |
| parents | 2d7595c8041d |
| children | a99bbda3cf1f |
| files | MetaRNASeq.R MetaRNAseq.xml Recount.R Recount.xml |
| diffstat | 4 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/MetaRNASeq.R Thu Jun 21 10:06:23 2018 -0400 +++ b/MetaRNASeq.R Thu Jun 21 10:41:50 2018 -0400 @@ -32,7 +32,7 @@ suppressPackageStartupMessages(require(VennDiagram)) suppressPackageStartupMessages(require(GEOquery)) -listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) +listInput <- trimws( unlist( strsplit(trimws(opt$input), "|") ) ) listfiles=vector() listfilenames=vector()
--- a/MetaRNAseq.xml Thu Jun 21 10:06:23 2018 -0400 +++ b/MetaRNAseq.xml Thu Jun 21 10:41:50 2018 -0400 @@ -24,7 +24,7 @@ Rscript ${__tool_directory__}/MetaRNASeq.R --input "#for $s in $studies: - ${s.input};${s.input.name};${s.nbreplicates}, + ${s.input};${s.input.name};${s.nbreplicates}| #end for " --fdr $fdr
--- a/Recount.R Thu Jun 21 10:06:23 2018 -0400 +++ b/Recount.R Thu Jun 21 10:41:50 2018 -0400 @@ -23,7 +23,7 @@ } #loading libraries -suppressPackageStartupMessages(require(GEOquery)) +suppressPackageStartupMessages(require(recount)) studyID=opt$id reportFile=opt$report @@ -40,8 +40,8 @@ { currentCount=as.data.frame(counts[,i]) sampleID=colnames(counts)[i] - colnames(currentCount)=sampleID - write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i]),sep="\t",row.names = T, col.names = T) + #colnames(currentCount)=sampleID + write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i],'.tabular'),sep="\t",row.names = T, col.names = F) } -write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t") \ No newline at end of file +write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t")
--- a/Recount.xml Thu Jun 21 10:06:23 2018 -0400 +++ b/Recount.xml Thu Jun 21 10:41:50 2018 -0400 @@ -15,20 +15,20 @@ <![CDATA[ Rscript --vanilla ${__tool_directory__}/Recount.R - --id ${RecountID} - --report ${Report} + --id ${recountID} + --report ${report} ]]> </command> <inputs> - <param name="RecountID" type="text" size="12" optional="false" label="GEOQuery ID" help=""> + <param name="recountID" type="text" size="12" optional="false" label="Recount ID" help=""> <validator type="empty_field"/> </param> </inputs> <outputs> <data format="txt" name="report"> - <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" /> + <discover_datasets pattern="__designation_and_ext__" format="tabular" directory="split" visible="true" /> </data> </outputs>