--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AffyQCnormalization.R	Thu Feb 22 08:38:22 2018 -0500
@@ -0,0 +1,128 @@
+#!/usr/bin/env Rscript
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("optparse")
+
+##### Read options
+option_list=list(
+		make_option("--input",type="character",default="NULL",help="rdata object containing eset object"),
+		make_option("--normalization",type="character",default=NULL,help="normalization method"),
+		make_option("--nbresult",type="character",default=NULL,help="number of result displayed results"),
+		make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
+		make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
+		make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
+		make_option("--htmltemplate",type="character",default=NULL,help="html template)")
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if(is.null(opt$input)){
+	print_help(opt_parser)
+	stop("input required.", call.=FALSE)
+}
+
+#loading libraries
+
+suppressPackageStartupMessages(require(Biobase))
+suppressPackageStartupMessages(require(GEOquery))
+suppressPackageStartupMessages(require(GEOmetadb))
+suppressPackageStartupMessages(require(limma))
+suppressPackageStartupMessages(require(jsonlite))
+suppressPackageStartupMessages(require(affy))
+suppressPackageStartupMessages(require(affyPLM))
+suppressPackageStartupMessages(require(dplyr))
+
+listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
+
+celList=vector()
+celFileNameList=vector()
+
+for (i in 1:length(listInput))
+{
+	inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
+	celList=c(celList,inputFileInfo[1])
+	celFileNameList=c(celFileNameList,inputFileInfo[2])
+}
+
+
+normalization=opt$normalization
+result_export_eset=opt$rdataoutput
+result=opt$htmloutput
+result.path=opt$htmloutputpath
+result.template=opt$htmltemplate
+
+dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
+for(i in 1:length(celList))
+{
+	file.copy(celList[i],paste0("./",celFileNameList[i]))
+}
+
+data <- ReadAffy(filenames=celFileNameList, celfile.path=".")
+htmlfile=readChar(result.template, file.info(result.template)$size)
+
+boxplot="boxplot.png"
+png(boxplot,width=800,height = 400)
+par(mar=c(7,5,1,1))
+boxplot(data,las=2,outline=FALSE)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
+file.copy(boxplot,result.path)
+
+images="images.png"
+nblines=length(celList)%/%4 + as.numeric((length(celList)%%4)!=0) 
+png(images,width=800,height = 200*nblines)
+par(mfrow=c(nblines,4))
+image(data)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###IMAGES###",replacement = images, fixed = TRUE)
+file.copy(images,result.path)
+
+
+plotMA="plotMA.png"
+nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) 
+png(plotMA,width=800,height =300*nblines )
+par(mfrow=c(nblines,3))
+MAplot(data)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###PLOTMA###",replacement = plotMA, fixed = TRUE)
+file.copy(plotMA,result.path)
+
+
+if (normalization == "rma") {
+	eset <- rma(data)
+} else if (normalization == "quantile") {
+	eset = rma(data,background = FALSE,normalize = TRUE)
+} else if (normalization == "background"){
+	eset = rma(data,background = TRUE ,normalize = FALSE)
+} else if (normalization == "log2") {
+	eset = rma(data,background = FALSE ,normalize = FALSE)
+}
+	
+
+boxplotnorm="boxplotnorm.png"
+png(boxplotnorm,width=800,height = 400)
+par(mar=c(7,5,1,1))
+boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
+file.copy(boxplotnorm,result.path)
+
+plotMAnorm="plotMAnorm.png"
+nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) 
+png(plotMAnorm,width=800,height =300*nblines )
+par(mfrow=c(nblines,3))
+#for (i in 1:length(celList)){
+MAplot(eset)
+#}
+
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
+file.copy(plotMAnorm,result.path)
+save(eset,file=result_export_eset)
+write(htmlfile,result)
+