changeset 8:d5ed62b4d3ac draft default tip

planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233

--- a/segmentFracB.R	Fri Apr 10 13:32:59 2020 +0000
+++ b/segmentFracB.R	Tue May 12 13:40:07 2020 +0000
@@ -1,14 +1,70 @@
+#!/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("--settings_type",type="character",default=NULL, dest="settingsType"),
+		make_option("--output_graph",type="character",default=NULL, dest="outputgraph"),
+		make_option("--zip_figures",type="character",default=NULL, dest="zipfigures"),
+		make_option("--settings_tumor",type="character",default=NULL, dest="settingsTypeTumor"),
+		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
+
 args<-commandArgs(TRUE)
 
-chrom=args[1]
-dataset=args[2]
-output=args[3]
-tmp_dir=args[4]
-input=args[5]
-outputfigures=type.convert(args[6])
-tumorcsv=args[7]
-user=args[8]
-method=args[9]
+chrom=opt$chrom
+datasetFile=opt$input
+output=opt$output
+tmp_dir=opt$new_file_path
+input=opt$settingsType
+outputfigures=type.convert(opt$outputgraph)
+tumorcsv=opt$settingsTypeTumor
+user=opt$userid
+method=opt$method
+log=opt$log
+outputlog=opt$outputlog
+outputgraph=opt$outputgraph
+zipfigures=opt$zipfigures
+
+#chrom=opt$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)
@@ -22,22 +78,67 @@
 	chrom_vec <- as.numeric(chrom_vecstring)
 }
 
-input_tmp <- strsplit(input,",")
-input_tmp_vecstring <-unlist(input_tmp)
+
+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]
+
 
 
-input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics",user)
+setwd(workdir)
 
-if (dataset == input) {
+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)
+}
+
+fig_dir = file.path("mpagenomics", user, "figures", dataset, "segmentation","fracB")
+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 (input == 'dataset') {
 	segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, savePlot=outputfigures, method=method)
 	
 } else {
+	input_tmp <- strsplit(input,",")
+	input_tmp_vecstring <-unlist(input_tmp)
+	input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
 	segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, savePlot=outputfigures, method=method)
 	
 }
-sink(output)
-print(format(segcall))
-sink()
-#write.table(segcall,output,row.names = FALSE, quote=FALSE, sep = "\t")
+write.table(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)
+}
 
-quit()
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+} 
+
+#sink(output)
+#print(format(segcall))
+#sink()
+
+

--- a/segmentFracB.py	Fri Apr 10 13:32:59 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-import os
-import sys
-import subprocess
-import zipfile
-import getopt
-
-
-def main(argv):
-       
-    try:
-        opts, args = getopt.getopt(argv,"hc:i:o:f:s:og:fig:t:p:l:u:m:",["chrom=","input=","output=","new_file_path=","settings_type=","output_graph=","zip_figures=","settings_tumor=","outputlog=","log=","userid=","method="])
-    except getopt.GetoptError as err:
-        print str(err)
-        sys.exit(2)
-    for opt, arg in opts:
-        if opt == '-h':
-            print 'extractCNopts.py'
-            sys.exit()
-        elif opt in ("-c", "--chrom"):
-            chromosome = arg
-        elif opt in ("-i", "--input"):
-            input_file = arg
-        elif opt in ("-o", "--output"):
-            output_file = arg
-        elif opt in ("-f", "--new_file_path"):
-            tmp_dir = arg
-        elif opt in ("-s", "--settings_type"):
-            input_type = arg
-        elif opt in ("-og", "--output_graph"):
-            output_graph = arg
-        elif opt in ("-fig", "--zip_figures"):
-            zip_file = arg
-        elif opt in ("-t", "--settings_tumor"):
-            tumorcsv = arg
-        elif opt in ("-p", "--outputlog"):
-            outputlog = arg
-        elif opt in ("-l", "--log"):
-            log = arg
-        elif opt in ("-u", "--userid"):
-            user_id = arg
-        elif opt in ("-m", "--method"):
-            method = arg
-  
-    script_dir=os.path.dirname(os.path.abspath(__file__))
-    
-    iFile=open(input_file,'r')
-    dataSetLine=iFile.readline()
-    dataset=dataSetLine.split("\t")[1]
-    iFile.close()
-      
-
-    if input_type=="dataset":
-        input_type=dataset
-
-    if (outputlog=="TRUE"):
-        errfile=open(log,'w')
-    else:
-        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
-    
-    fig_dir=os.path.join("mpagenomics",user_id,"figures",dataset,"segmentation/fracB")
-
-    abs_fig_dir=os.path.join(tmp_dir,fig_dir)
-    if (os.path.isdir(abs_fig_dir)) and (output_graph=="TRUE"):
-        old_files=os.listdir(abs_fig_dir)
-        for ifile in old_files:
-            os.remove(os.path.join(abs_fig_dir,ifile))
-           
-        
-    retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segmentFracB.R"),  chromosome, dataset, output_file, tmp_dir, input_type, output_graph, tumorcsv, user_id, method], stdout = errfile, stderr = errfile)
-    
-    errfile.close()
-     
-    if (retcode == 0):
-        if (os.path.isdir(abs_fig_dir)) and (output_graph=="TRUE"):
-        
-            new_files=os.listdir(abs_fig_dir)
-            zipbuf = zipfile.ZipFile(os.path.join(abs_fig_dir,zip_file), 'w', zipfile.ZIP_DEFLATED)
-            for current_file in new_files:
-                fn = os.path.join(abs_fig_dir,current_file)
-                relfn=fn[len(abs_fig_dir)+len(os.sep):]
-                zipbuf.write(fn,relfn)
-        sys.exit(retcode)
-    else:
-        sys.exit(retcode)
-
-if __name__ == "__main__":
-    main(main(sys.argv[1:]))

--- a/segmentFracB.xml	Fri Apr 10 13:32:59 2020 +0000
+++ b/segmentFracB.xml	Tue May 12 13:40:07 2020 +0000
@@ -1,24 +1,27 @@
-<tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True">
+<tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True" version="1.0.0">
   <description></description>
-  <command interpreter="python">
-    segmentFracB.py 
-  	--chrom '$chrom' 
-  	--input '$input' 
-  	--output '$output' 
-  	--new_file_path '$__new_file_path__'
-  	#if $settings.settingsType == "file":
-  	--settings_type '$settings.inputs'
-  	#end if
-  	#if $settings.settingsType == "dataset":
-  	--settings_type '$settings.settingsType'
-  	#end if
-  	--output_graph '$outputgraph' 
-  	--zip_figures '$zipfigures'
-  	--settings_tumor '$tumorcsv'
-  	--outputlog '$outputlog' 
-  	--log '$log' 
-  	--userid '$__user_id__' 
-  	--method '$method'
+  <command>
+    <![CDATA[ 
+        Rscript
+        ${__tool_directory__}/segmentFracB.R  
+  		--chrom '$chrom' 
+  		--input '$input' 
+  		--output '$output' 
+  		--new_file_path '$__new_file_path__'
+  		#if $settings.settingsType == "file":
+  			--settings_type '$settings.inputs'
+  		#end if
+  		#if $settings.settingsType == "dataset":
+  			--settings_type '$settings.settingsType'
+  		#end if
+  		--output_graph '$outputgraph' 
+  		--zip_figures '$zipfigures'
+  		--settings_tumor '$tumorcsv'
+  		--outputlog '$outputlog' 
+  		--log '$log' 
+  		--userid '$__user_id__' 
+  		--method '$method'
+  	]]>
   </command>
   <inputs>
    	<param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>

--- a/selection.R	Fri Apr 10 13:32:59 2020 +0000
+++ b/selection.R	Tue May 12 13:40:07 2020 +0000
@@ -1,26 +1,71 @@
-args<-commandArgs(TRUE)
+#!/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")
+);
 
-input=args[1]
-dataResponse=args[2]
-chrom=args[3]
-tmp_dir=args[4]
-signal=args[5]
-snp=type.convert(args[6])
-settingsType=args[7]
-tumor=args[8]
-fold=as.integer(args[9])
-loss=args[10]
-plot=type.convert(args[11])
-output=args[12]
-user=args[13]
-package=args[14]
+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") {
@@ -31,18 +76,23 @@
 		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=plot, nbFolds=fold, pkg=package)
+			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=plot, nbFolds=fold,pkg=package)	
+			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=plot, nbFolds=fold,pkg=package)
+		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=plot, nbFolds=fold,pkg=package)
+  		res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package)
 		}
 }
 
@@ -63,12 +113,22 @@
   }
 }
 
+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")
+	#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)
 

--- a/selection.py	Fri Apr 10 13:32:59 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-import os
-import sys
-import subprocess
-import shutil
-
-def main():
-
-    input_file=sys.argv[1]
-    tmp_dir=sys.argv[4]
-    script_dir=os.path.dirname(os.path.abspath(__file__))
-    plot=sys.argv[11]
-    pdffigures=sys.argv[13]
-    outputlog=sys.argv[14]
-    log=sys.argv[15]
-    user=sys.argv[16]
-    package=sys.argv[17]
-        
-    iFile=open(input_file,'r')
-    dataSetLine=iFile.readline()
-    dataset=dataSetLine.split("\t")[1]
-    iFile.close()    
-        
-    if (outputlog=="TRUE"):
-        errfile=open(log,'w')
-    else:
-        errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
-    
-    retcode=subprocess.call(["Rscript", os.path.join(script_dir,"selection.R"), dataset, sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6], sys.argv[7], sys.argv[8], sys.argv[9], sys.argv[10], sys.argv[11], sys.argv[12],sys.argv[16],package], stdout = errfile, stderr = errfile)
-    
-    if (plot=="TRUE"):
-        shutil.copy(os.path.join(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures)
-    
-    errfile.close()
-       
-    sys.exit(retcode)
-
-if __name__ == "__main__":
-    main()

--- a/selection.xml	Fri Apr 10 13:32:59 2020 +0000
+++ b/selection.xml	Tue May 12 13:40:07 2020 +0000
@@ -1,26 +1,41 @@
 <tool id="selection" name="Markers selection" force_history_refresh="True" version="0.1.0">
-  <command interpreter="python">
-    selection.py '$input'  '$response' '$chromosome' '$__new_file_path__' '$settingsSNP.signal'
+  <command>
+    <![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/selection.R 
+  	 --input '$input'  
+  	 --response '$response' 
+  	 --chrom '$chromosome' 
+  	 --new_file_path '$__new_file_path__' 
+  	 --settingsSignal '$settingsSNP.signal'
   	#if $settingsSNP.signal == "CN":
-  	'$settingsSNP.snp' 
+  	 --settingsSnp '$settingsSNP.snp' 
   	#end if
   	#if $settingsSNP.signal == "fracB":
-  	'none'
+  	 --settingsSnp 'none'
   	#end if
-  	'$settings.settingsType'
+  	 --settingsType '$settings.settingsType'
   	#if $settings.settingsType == "tumor":
-  	'$tumorcsv' 
+  	 --settingsType '$tumorcsv' 
   	#end if
   	#if $settings.settingsType == "standard":
-  	'none'
+  	 --settingsType 'none'
   	#end if
-  	'$folds' '$settingsLoss.loss' '$outputgraph' '$output' '$pdffigures' '$outputlog' '$log' '$__user_id__'
+  	 --folds '$folds' 
+  	 --settingsLoss '$settingsLoss.loss' 
+  	 --outputgraph '$outputgraph' 
+  	 --output '$output' 
+  	 --pdffigures '$pdffigures' 
+  	 --outputlog '$outputlog' 
+  	 --log '$log' 
+  	 --userId '$__user_id__'
   	#if $settingsLoss.loss == "linear":
-  	'$settingsLoss.package' 
+  	 --settingsPackage '$settingsLoss.package' 
   	#end if
   	#if $settingsLoss.loss == "logistic":
-  	'HDPenReg'
+  	 --settingsPackage'HDPenReg'
   	#end if
+  	]]>
   </command>
   <inputs>
     <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
@@ -103,7 +118,7 @@
     
     </inputs>        
   <outputs>
-  	<data format="txt" name="output" label="selection of ${input.name}" />
+  	<data format="tabular" name="output" label="selection of ${input.name}" />
     <data format="pdf" name="pdffigures" label="figures of SNPs selection of ${input.name}">
     	<filter>outputgraph == "TRUE"</filter>
     	<filter>(settingsLoss['package'] != 'spikeslab')</filter>	

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selectionExtracted.R	Tue May 12 13:40:07 2020 +0000
@@ -0,0 +1,89 @@
+#!/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("--response",type="character",default=NULL, dest="response"),
+		make_option("--loss",type="character",default=NULL, dest="loss"),
+		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")
+);
+
+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
+response=opt$response
+output=opt$output
+tmp_dir=opt$new_file_path
+nbFolds=as.numeric(opt$folds)
+loss=opt$loss
+log=opt$log
+outputlog=opt$outputlog
+
+
+#args<-commandArgs(TRUE)
+#
+#input=args[1]
+#response=args[2]
+#tmp_dir=args[3]
+#nbFolds=as.numeric(args[4])
+#loss=args[5]
+#output=args[6]
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics")
+setwd(workdir)
+
+if (outputlog){
+	sinklog <- file(log, open = "wt")
+	sink(sinklog ,type = "output")
+	sink(sinklog, type = "message")
+} 
+
+CN=read.table(input,header=TRUE,check.names=FALSE)
+drops=c("chromosome","position","probeName")
+CNsignal=CN[,!(names(CN)%in% drops)]
+samples=names(CNsignal)
+CNsignalMatrix=t(data.matrix(CNsignal))
+resp=read.table(response,header=TRUE,sep=",")
+listOfFile=resp[[1]]
+responseValue=resp[[2]]
+index = match(listOfFile,rownames(CNsignalMatrix))
+responseValueOrder=responseValue[index]
+
+result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE)
+
+CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)]
+
+CNsignalResult["coefficient"]=result$coefficient
+CNsignalResult["index"]=result$markers.index
+
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+} 
+
+#sink(output)
+#print(format(CNsignalResult),row.names=FALSE)
+#sink()
+write.table(CNsignalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selectionExtracted.xml	Tue May 12 13:40:07 2020 +0000
@@ -0,0 +1,111 @@
+<tool id="markersSelection" name="Markers selection" force_history_refresh="True" version="0.1.0">
+  <description> of previously extracted signal</description>
+  <command>
+  	<![CDATA[ 
+        Rscript 
+        ${__tool_directory__}/selectionExtracted.R 
+    --input '$input' 
+  	--response '$response' 
+  	--new_file_path '$__new_file_path__' 
+  	--folds '$folds' 
+  	--loss '$loss' 
+  	--outputlog '$outputlog' 
+  	--output '$output' 
+  	--log '$log'
+  	]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="sef" label="Input Signal" help="see below for more information on file format"/>
+	<param name="response" type="data" format="csv" label="Data response" help="Data response csv file. See below for more information on file format" />    
+	<param name="folds" type="integer" min="1" value="10" label ="Number of folds for cross validation" help="Integer between 1 and number of file in the .cel file dataset"/>
+    <param name="loss" type="select" multiple="false" label="Response type">
+      	<option value="linear">Linear</option>
+    	<option value="logistic">Logistic</option>
+    </param>
+   
+	<param name="outputgraph" type="select" label="Output figures">
+        <option value="TRUE">Yes</option>
+        <option value="FALSE">No</option>
+     </param>    
+    <param name="outputlog" type="select" label="Output log">
+        <option value="TRUE">Yes</option>
+        <option value="FALSE">No</option>
+    </param>    
+  </inputs>       
+  <outputs>
+    <data format="tabular" name="output" label="selection of ${input.name}" />
+    <data format="log" name="log" label="log of selection of ${input.name}" >
+    	<filter>outputlog == "TRUE"</filter>
+    </data>
+  </outputs>
+  <stdio>
+    <exit_code range="1:"   level="fatal"   description="See logs for more details" />
+   </stdio>
+  <help>
+  **What it does**
+   	    	
+This tool selects some relevant markers according to a response using penalized regressions.
+  
+Input:
+
+*A tabular text file containing 3 fixed columns and 1 column per sample:*
+	
+	- chr: Chromosome.
+	- position: Genomic position (in bp).
+  	- probeNames: Names of the probes.
+  	- One column per sample which contain the copy number signal for each sample.
+
+Output:
+  	
+*A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):*
+	
+	- chr: Chromosome containing the selected SNP.
+  	- position: Position of the selected SNP.
+	- index: Index of the selected SNP.
+	- names: Name of the selected SNP.
+	- coefficient: Regression coefficient of the selected SNP.
+
+-----
+
+**Data Response csv file**
+     	
+Data response csv file format:
+	
+	- The first column contains the names of the different files of the dataset.
+     	 
+	- The second column is the response associated with each file. 
+     	
+	- Column names of these two columns are respectively files and response.
+
+	- Columns are separated by a comma
+     	
+	- *Extensions of the files (.CEL for example) should be removed*
+
+
+     	
+**Example** 
+
+Let 3 .cel files in the studied dataset ::
+     	
+     	patient1.cel
+     	patient2.cel
+     	patient3.cel 
+     	
+The csv file should look like this ::
+     	
+     	files,response
+     	patient1,1.92145
+     	patient2,2.12481
+     	patient3,1.23545
+
+
+-----
+  	   	
+**Citation**
+	
+If you use this tool please cite : 
+
+`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
+  
+ </help>
+</tool>