--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ImportDataFromMatrix.R	Thu Feb 22 08:38:22 2018 -0500
@@ -0,0 +1,114 @@
+#!/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("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
+		make_option("--normalization",type="character",default=NULL,help="log2 transformation"),
+		make_option("--annotations",type="character",default="NULL",help="rdata object containing eset object"),
+		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$input)){
+	print_help(opt_parser)
+	stop("input required.", call.=FALSE)
+}
+
+if(is.null(opt$conditions)){
+	print_help(opt_parser)
+	stop("conditions input required.", call.=FALSE)
+}
+
+
+#loading libraries
+suppressPackageStartupMessages(require(GEOquery))
+
+suppressPackageStartupMessages(require(Biobase))
+suppressPackageStartupMessages(require(GEOquery))
+suppressPackageStartupMessages(require(GEOmetadb))
+suppressPackageStartupMessages(require(limma))
+suppressPackageStartupMessages(require(jsonlite))
+suppressPackageStartupMessages(require(affy))
+suppressPackageStartupMessages(require(dplyr))
+suppressPackageStartupMessages(require(affyPLM))
+
+dataFile=opt$input
+normalization=opt$normalization
+conditionsFile=opt$conditions
+annotation=opt$annotations
+result_export_eset=opt$rdataoutput
+result=opt$htmloutput
+result.path=opt$htmloutputpath
+result.template=opt$htmltemplate
+
+dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
+
+data=as.matrix(read.table(file = dataFile,row.names=1,header=TRUE))
+conditions=read.table(file=conditionsFile,sep = "\t",row.names=1)
+htmlfile=readChar(result.template, file.info(result.template)$size)
+
+colnames(conditions)=c("source_name_ch1","description")
+phenodata<-new("AnnotatedDataFrame",data=conditions)
+
+head(data)
+conditions
+
+eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
+
+if (normalization == "quantile") {
+	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2")
+} else if (normalization == "log2") {
+	exprs(eset) = log2(exprs(eset)) 
+} 
+
+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(colnames(data))%/%3 + as.numeric((length(colnames(data))%%3)!=0) 
+png(plotMAnorm,width=800,height =300*nblines )
+par(mfrow=c(nblines,3))
+##for (i in 1:length(colnames(data))){
+	MAplot(eset)
+#}
+
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
+file.copy(plotMAnorm,result.path)
+#write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
+#saveConditions=c(condition1Name,condition2Name)
+save(eset,file=result_export_eset)
+write(htmlfile,result)
+
+#l=list()
+#for(i in 1:length(esets))
+#{
+#	l[[paste("study",i,sep="")]]<-res[[i]]
+#}
+#l[["Meta"]]=res[[length(res)-1]]
+#showVenn(res,file.path(temp.files.path,"venn.png"))
+#writeLines(c("<h2>Venn diagram</h2>"),file.conn)
+#writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
+#writeLines(c("</body></html>"),file.conn)
+#close(file.conn)
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