--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selection.R	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,135 @@
+#!/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("--chrom",type="character",default=NULL, dest="chrom"),
+		make_option("--input",type="character",default=NULL, dest="input"),
+		make_option("--output",type="character",default=NULL, dest="output"),
+		make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"),
+		make_option("--response",type="character",default=NULL, dest="response"),
+		make_option("--settingsType",type="character",default=NULL, dest="settingsType"),
+		make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"),
+		make_option("--settingsSnp",type="character",default=NULL, dest="settingsSnp"),
+		make_option("--settingsSignal",type="character",default=NULL, dest="settingsSignal"),
+		make_option("--settingsLoss",type="character",default=NULL, dest="settingsLoss"),
+		make_option("--pdffigures",type="character",default=NULL, dest="pdffigures"),
+		make_option("--folds",type="character",default=NULL, dest="folds"),
+		make_option("--outputlog",type="character",default=NULL, dest="outputlog"),
+		make_option("--log",type="character",default=NULL, dest="log"),
+		make_option("--userId",type="character",default=NULL, dest="userid"),
+		make_option("--settingsPackage",type="character",default=NULL, dest="settingsPackage")
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if(is.null(opt$input)){
+	print_help(opt_parser)
+	stop("input required.", call.=FALSE)
+}
+
+#loading libraries
+
+
+chrom=opt$chrom
+dataset=opt$input
+dataResponse=opt$response
+output=opt$output
+tmp_dir=opt$new_file_path
+signal=opt$settingsSignal
+settingsType=opt$settingsType
+outputfigures=type.convert(opt$outputgraph)
+snp=type.convert(opt$settingsSnp)
+user=opt$userid
+folds=as.numeric(opt$folds)
+loss=opt$settingsLoss
+log=opt$log
+outputlog=opt$outputlog
+outputgraph=opt$outputgraph
+pdffigures=opt$pdffigures
+package=opt$settingsPackage
+
+
+library(MPAgenomics)
+library(glmnet)
+library(spikeslab)
+library(lars)
+
+inputDataset=read.table(file=dataset,stringsAsFactors=FALSE)
+input=inputDataset[1,2]
+workdir=file.path(tmp_dir, "mpagenomics",user)
+print(workdir)
+setwd(workdir)
+
+if (grepl("all",tolower(chrom)) | chrom=="None") {
+		chrom_vec=c(1:25)
+	} else {
+		chrom_tmp <- strsplit(chrom,",")
+		chrom_vecstring <-unlist(chrom_tmp)
+		chrom_vec <- as.numeric(chrom_vecstring)
+	}
+
+if (outputlog){
+	sinklog <- file(log, open = "wt")
+	sink(sinklog ,type = "output")
+	sink(sinklog, type = "message")
+} 
+
+if (settingsType == "tumor") {
+	if (signal=="CN") {
+			res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, normalTumorArray=tumor, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds, pkg=package)
+		} else {
+			res=markerSelection(input,dataResponse, chromosome=chrom_vec,signal=signal,normalTumorArray=tumor, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)	
+		} 
+} else {
+	if (signal=="CN") {
+		res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
+		} else {
+  		res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
+		}
+}
+
+res
+
+df=data.frame()
+list_chr=names(res)
+markerSelected=FALSE
+
+for (i in list_chr) {
+  chr_data=res[[i]]
+  len=length(chr_data$markers.index)
+  if (len != 0)
+  {
+	markerSelected=TRUE
+	chrdf=data.frame(rep(i,len),chr_data$markers.position,chr_data$markers.index,chr_data$markers.names,chr_data$coefficient)
+  	df=rbind(df,chrdf)
+  }
+}
+
+if (outputgraph){
+	file.rename(file.path(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures)
+}
+
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+} 
+
+if (markerSelected) {
+	colnames(df) <- c("chr","position","index","names","coefficient")
+	#sink(output)
+	#print(format(df),row.names=FALSE)
+	#sink()
+	write.table(df,output,row.names = FALSE, quote = FALSE, sep = "\t")
+} else 
+	writeLines("no SNP selected", output)
+
+