--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/probmetab.r	Mon Jul 04 04:29:25 2016 -0400
@@ -0,0 +1,119 @@
+#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
+# probmetab.r version="1.0.0"
+# Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
+
+
+# ----- LOG -----
+log_file=file("probmetab.log", open = "wt")
+sink(log_file)
+sink(log_file, type = "out")
+
+# ----- PACKAGE -----
+cat("\tPACKAGE INFO\n")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
+for(p in pkgs) {
+	suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
+	cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
+}
+
+source_local <- function(fname){
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+cat("\n\n")
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n") 
+listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
+
+
+
+# ----- PROCESSING INFILE -----
+cat("\tINFILE PROCESSING INFO\n")
+
+# ----- INFILE PROCESSING -----
+
+if(listArguments[["mode_acquisition"]]=="one") {
+	load(listArguments[["xa"]])
+    
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+	
+    #Unzip the chromatograms file for plotting EIC pour the HTML file
+	if(exists("zipfile"))
+	{
+		if (zipfile!=""){
+			directory=unzip(zipfile)
+		}
+	}	
+	if (!exists("xa")) {
+		xa=xsAnnotate_object
+	}
+	source_local("lib.r")
+	if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
+	
+} else if(listArguments[["inputs_mode"]]=="two"){
+	load(listArguments[["image_pos"]])
+    
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+    
+	#Unzip the chromatograms file for plotting EIC pour the HTML file
+	if(exists("zipfile")) {
+		if (zipfile!=""){
+			directory=unzip(zipfile)
+		}
+	}
+	if (!exists("xa")) {
+		xa=xsAnnotate_object
+	}
+	xaP=xa
+	source_local("lib.r")	
+	if (!exists("variableMetadata")) variableMetadataP= getVariableMetadata(xa)
+	else variableMetadataP=variableMetadata
+
+
+	load(listArguments[["image_neg"]])
+    
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+    
+	#Unzip the chromatograms file for plotting EIC pour the HTML file
+	if(exists("zipfile")) {
+		
+	 	if (zipfile!=""){
+			directory=unzip(zipfile)
+		}
+	}
+	if (!exists("xa")) {
+		xa=xsAnnotate_object
+	}
+	xaN=xa
+	source_local("lib.r")
+	
+	if (!exists("variableMetadata")) variableMetadataN= getVariableMetadata(xa)
+	else variableMetadataN=variableMetadata
+}
+
+#Import the different functions
+source_local("lib.r")
+source_local("export.class.table-color-graph.R")
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+if(listArguments[["mode_acquisition"]]=="one") {
+	results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
+} else if(listArguments[["inputs_mode"]]=="two"){
+	results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
+}
+#delete the parameters to avoid the passage to the next tool in .RData image
+#rm(listArguments)
+cat("\tDONE\n")
+#saving R data in .Rdata file to save the variables used in the present tool
+#save.image(paste("probmetab","RData",sep="."))
+