--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.R	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,67 @@
+#!/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, 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("--length",type="character",default=NULL, dest="length"),
+		make_option("--probes",type="character",default=NULL, dest="probes"),
+		make_option("--outputlog",type="character",default=NULL, dest="outputlog"),
+		make_option("--log",type="character",default=NULL, dest="log")
+	);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if(is.null(opt$input)){
+	print_help(opt_parser)
+	stop("input required.", call.=FALSE)
+}
+
+#loading libraries
+
+input=opt$input
+output=opt$output
+tmp_dir=opt$new_file_path
+nbcall=opt$nbcall
+length=as.numeric(opt$length)
+probes=as.numeric(opt$probes)
+log=opt$log
+outputlog=opt$outputlog
+
+if (outputlog){
+	sinklog <- file(log, open = "wt")
+	sink(sinklog ,type = "output")
+	sink(sinklog, type = "message")
+} 
+
+nbcall_tmp <- strsplit(nbcall,",")
+nbcall_vecstring <-unlist(nbcall_tmp)
+
+nbcall_vecstring
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics")
+setwd(workdir)
+
+segcall = read.table(input, header = TRUE)
+filtercall=filterSeg(segcall,length,probes,nbcall_vecstring)
+#sink(output)
+#print(format(filtercall),row.names=FALSE)
+#sink()
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+} 
+write.table(filtercall,output,row.names = FALSE, quote = FALSE, sep = "\t")
+