diff MetaRNASeq.R @ 35:a99bbda3cf1f draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit e956e308e78c1c2d2c5ac7420621527f0d4dad28

--- a/MetaRNASeq.R	Thu Jun 21 10:41:50 2018 -0400
+++ b/MetaRNASeq.R	Thu Jun 21 11:20:56 2018 -0400
@@ -10,7 +10,9 @@
 ##### Read options
 option_list=list(
 		make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"),
-		make_option("--fdr",type="character",default=NULL,help="Adjusted p-value threshold to be declared differentially expressed"),
+		make_option("--inputName",type="character",default=NULL,help="filenames of the Rddata objects"),
+                make_option("--nbreplicates",type="character",default=NULL,help="number of replicate per study"),
+                make_option("--fdr",type="character",default=NULL,help="Adjusted p-value threshold to be declared differentially expressed"),
 		make_option("--result",type="character",default=NULL,help="text file containing result of the meta-analysis"),
 		make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
 		make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
@@ -32,19 +34,23 @@
 suppressPackageStartupMessages(require(VennDiagram))
 suppressPackageStartupMessages(require(GEOquery))
 
-listInput <- trimws( unlist( strsplit(trimws(opt$input), "|") ) )
+listfiles <- trimws( unlist( strsplit(trimws(opt$input), ";") ) )
+listfilenames <- trimws( unlist( strsplit(trimws(opt$inputName), ";") ) )
+nbreplicates <- as.numeric(trimws( unlist( strsplit(trimws(opt$nbreplicates), ";") ) ))
 
-listfiles=vector()
-listfilenames=vector()
-nbreplicates=vector()
+listfiles
+listfilenames
+nbreplicates
+
 
-for (i in 1:length(listInput))
-{
-	inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
-	listfiles=c(listfiles,inputFileInfo[1])
-	listfilenames=c(listfilenames,inputFileInfo[2])
-	nbreplicates[i]=as.numeric(inputFileInfo[3])
-}
+
+#for (i in 1:length(listInput))
+#{
+#	inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
+#	listfiles=c(listfiles,inputFileInfo[1])
+#	listfilenames=c(listfilenames,inputFileInfo[2])
+#	nbreplicates[i]=as.numeric(inputFileInfo[3])
+#}
 
 
 outputfile <- opt$result
@@ -52,6 +58,9 @@
 html.files.path=opt$htmloutputpath
 result.template=opt$htmltemplate
 
+
+html.files.path
+
 alpha=as.numeric(opt$fdr)
 
 listData=lapply(listfiles,read.table)
@@ -106,6 +115,7 @@
 library(VennDiagram)
 DE_num=apply(keepDE[,1:(length(listfiles)+2)], 2, FUN=function(x) which(x==1))
 #DE_num=apply(DEresults, 2, FUN=function(x) which(x==1))
+dir.create(html.files.path, showWarnings = TRUE, recursive = FALSE)
 temp.venn.plot = file.path( html.files.path, paste("venn.png"))
 if (length(listfiles)<=2) {
 	title="VENN DIAGRAM"