# HG changeset patch
# User fubar
# Date 1374902720 14400
# Node ID 8c0405de0695da0cc1b058db442319e33dfe3e01
# Parent  cd586457aced119de791321b47d4da5d8b0551f5
Uploaded

diff -r cd586457aced -r 8c0405de0695 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:07:52 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:25:20 2013 -0400
@@ -93,7 +93,15 @@
     </param>
   </inputs>
   <outputs>
-    <data format="tabular" name="outtab" label="${title}.xls"/>
+    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
+         <filter>edgeR.doedgeR == "T"</filter>
+    </data>
+    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
+         <filter>DESeq2.doDESeq2 == "T"</filter>
+    </data>
+    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
+         <filter>doVoom == "T"</filter>
+    </data>
     <data format="html" name="html_file" label="${title}.html"/>
   </outputs>
  <stdio>
@@ -367,7 +375,7 @@
 
 
 
-edgeIt = function (Count_Matrix,group,outputfilename,fdrtype='fdr',priordf=5, 
+edgeIt = function (Count_Matrix,group,out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
         fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
         filterquantile=0.2, subjects=c(),mydesign=NULL,
         doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
@@ -504,7 +512,7 @@
   print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
   nzd = data.frame(log(nonzerod + 1e-2,10))
   boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf")
-  write.table(soutput,outputfilename, quote=FALSE, sep="\t",row.names=F)
+  write.table(soutput,out_edgeR, quote=FALSE, sep="\t",row.names=F)
   tt = cbind( 
     Name=as.character(rownames(DGEList\$counts)),
     DE\$table,
@@ -559,7 +567,7 @@
     qqPlot(descr=paste(myTitle,'DESeq2 qqplot'),pvector=rDESeq\$pvalue,outpdf='DESeq2_qqplot.pdf')
     cat("# DESeq top 50\n")
     print.noquote(srDESeq[1:50,])
-    write.table(srDESeq,paste(mt,'DESeq2_TopTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
+    write.table(srDESeq,out_DESeq2, quote=FALSE, sep="\t",row.names=F)
     topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
     DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
     DESeqcounts = rep(0, length(allgenes))
@@ -605,7 +613,7 @@
       rownames(rvoom) = rownames(workCM)
       rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
       srvoom = rvoom[order(rvoom\$P.Value),]
-      write.table(srvoom,paste(mt,'VOOM_topTable.xls',sep='_'), quote=FALSE, sep="\t",row.names=F)
+      write.table(srvoom,out_VOOM, quote=FALSE, sep="\t",row.names=F)
       # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
       topresults.voom = srvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
       voomcountsindex = which(allgenes %in% topresults.voom\$ID)
@@ -651,6 +659,9 @@
 ###sink(stdout(),append=T,type="message")
 builtin_gmt=""
 history_gmt=""
+out_edgeR = F
+out_DESeq2 = F
+out_VOOM = F
 doDESeq2 = $DESeq2.doDESeq2 # make these T or F
 doVoom = $doVoom
 doCamera = F 
@@ -658,12 +669,16 @@
 edgeR_priordf = 0
 
 #if $DESeq2.doDESeq2 == "T"
+  out_DESeq2 = "$out_DESeq2"
   DESeq_fitType = "$DESeq2.DESeq_fitType"
 #end if
 #if $edgeR.doedgeR == "T"
-edgeR_priordf = $edgeR.edgeR_priordf
+  out_edgeR = "$out_edgeR"
+  edgeR_priordf = $edgeR.edgeR_priordf
 #end if
-
+#if $doVoom == "T"
+  out_VOOM = "$out_VOOM"
+#end if
 
 Out_Dir = "$html_file.files_path"
 Input =  "$input1"
@@ -716,7 +731,7 @@
 group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
 group = factor(group, levels=c(ControlName,TreatmentName))
 colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
-results = edgeIt(Count_Matrix=Count_Matrix,group=group,outputfilename=outputfilename,
+results = edgeIt(Count_Matrix=Count_Matrix,group=group,out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2,
                  fdrtype='BH',priordf=edgeR_priordf,fdrthresh=0.05,outputdir='.',
                  myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=c(),
                  doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,