# HG changeset patch
# User sblanck
# Date 1529592110 14400
# Node ID 0a74b8de4c106b7a7d44fe0f27e8f619c5a24f74
# Parent  2d7595c8041d46e564ce8e8d695bbc6b0e317a27
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 288d0dce1c0877bf9c3431a581d638b0ac336d3f

diff -r 2d7595c8041d -r 0a74b8de4c10 MetaRNASeq.R
--- 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()
diff -r 2d7595c8041d -r 0a74b8de4c10 MetaRNAseq.xml
--- 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
diff -r 2d7595c8041d -r 0a74b8de4c10 Recount.R
--- 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")
diff -r 2d7595c8041d -r 0a74b8de4c10 Recount.xml
--- 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>