--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segcall.R	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,124 @@
+#!/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("--nbcall",type="character",default=NULL, dest="nbcall"),
+		make_option("--settingsType",type="character",default=NULL, dest="settingsType"),
+		make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"),
+		make_option("--snp",type="character",default=NULL, dest="snp"),
+		make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"),
+		make_option("--settingsTypeTumor",type="character",default=NULL, dest="settingsTypeTumor"),
+		make_option("--cellularity",type="character",default=NULL, dest="cellularity"),
+		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("--method",type="character",default=NULL, dest="method")
+);
+
+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
+datasetFile=opt$input
+output=opt$output
+tmp_dir=opt$new_file_path
+nbcall=as.numeric(opt$nbcall)
+settingsType=opt$settingsType
+outputfigures=type.convert(opt$outputgraph)
+snp=type.convert(opt$snp)
+tumorcsv=opt$settingsTypeTumor
+cellularity=as.numeric(opt$cellularity)
+user=opt$userid
+method=opt$method
+log=opt$log
+outputlog=opt$outputlog
+outputgraph=opt$outputgraph
+zipfigures=opt$zipfigures
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics",user)
+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")
+} 
+	
+	
+inputDataset=read.table(file=datasetFile,stringsAsFactors=FALSE)
+dataset=inputDataset[1,2]
+
+fig_dir = file.path("mpagenomics", user, "figures", dataset, "segmentation","CN")
+abs_fig_dir = file.path(tmp_dir, fig_dir)
+
+if (outputgraph) {
+	if (dir.exists(abs_fig_dir)) {
+		system(paste0("rm -r ", abs_fig_dir))
+	}
+}
+
+if (settingsType == 'dataset') {
+	if (tumorcsv== "none")
+	{
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
+  	} else {
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
+  	}
+} else {
+	input_tmp <- strsplit(settingsType,",")
+	input_tmp_vecstring <-unlist(input_tmp)
+	input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+  	if (tumorcsv== "none") 
+  	{
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
+  	} else {
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
+  	}
+}
+
+
+write.table(format(segcall),output,row.names = FALSE, quote=FALSE, sep = "\t")
+
+
+if (outputgraph) {	
+	setwd(abs_fig_dir)
+	files2zip <- dir(abs_fig_dir)
+	zip(zipfile = "figures.zip", files = files2zip)
+	file.rename("figures.zip",zipfigures)
+}
+
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+} 
+#write.fwf(segcall,output,rownames = FALSE, quote=FALSE, sep = "\t")
+