--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipo4xcmsSet.r	Thu Aug 03 06:00:00 2017 -0400
@@ -0,0 +1,163 @@
+#!/usr/bin/env Rscript
+#Authors Gildas Le Corguille and Yann Guitton
+
+
+# ----- LOG FILE -----
+log_file=file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+options(bitmapType='cairo')
+cat("\tPACKAGE INFO\n")
+#pkgs=c("xcms","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","rsm","igraph","CAMERA","IPO","snow","batch")
+for(pkg in pkgs) {
+  suppressWarnings( suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
+  cat(pkg,"\t",as.character(packageVersion(pkg)),"\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')
+
+cat("\n\n");
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+
+#Import the different functions
+source_local("lib.r")
+
+cat("\n\n")
+
+#Import the different functions
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+xsetRdataOutput = paste("ipo4xcmsSet","RData",sep=".")
+if (!is.null(listArguments[["xsetRdataOutput"]])){
+  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
+}
+
+parametersOutput = "parametersOutput.tsv"
+if (!is.null(listArguments[["parametersOutput"]])){
+  parametersOutput = listArguments[["parametersOutput"]]; listArguments[["parametersOutput"]]=NULL
+}
+
+samplebyclass = 2
+if (!is.null(listArguments[["samplebyclass"]])){
+  samplebyclass = listArguments[["samplebyclass"]]; listArguments[["samplebyclass"]]=NULL
+}
+
+#necessary to unzip .zip file uploaded to Galaxy
+#thanks to .zip file it's possible to upload many file as the same time conserving the tree hierarchy of directories
+
+
+if (!is.null(listArguments[["zipfile"]])){
+  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+}
+
+
+if (!is.null(listArguments[["singlefile_galaxyPath"]])){
+    singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL
+    singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL
+}
+
+# single file case
+#@TODO: need to be refactoring
+if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
+    if(!file.exists(singlefile_galaxyPath)){
+        error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
+        print(error_message); stop(error_message)
+    }
+    
+    cwd=getwd()
+    dir.create("raw")
+    setwd("raw")
+    file.symlink(singlefile_galaxyPath,singlefile_sampleName)
+    setwd(cwd)
+    
+    directory = "raw"
+    
+}
+
+# We unzip automatically the chromatograms from the zip files.
+if(exists("zipfile") && (zipfile!="")) {
+    if(!file.exists(zipfile)){
+        error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
+        print(error_message)
+        stop(error_message)
+    }
+
+    #list all file in the zip file
+    #zip_files=unzip(zipfile,list=T)[,"Name"]
+
+    # Because IPO only want raw data in its working directory
+    dir.create("ipoworkingdir")
+    setwd("ipoworkingdir")
+
+    #unzip
+    suppressWarnings(unzip(zipfile, unzip="unzip"))
+
+    #get the directory name
+    filesInZip=unzip(zipfile, list=T);
+    directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
+    directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
+    directory = "."
+    if (length(directories) == 1) directory = directories
+
+    cat("files_root_directory\t",directory,"\n")
+
+
+}
+
+#addition of the directory to the list of arguments in the first position
+checkXmlStructure(directory)
+checkFilesCompatibilityWithXcms(directory)
+
+cat("\n\n")
+
+
+
+
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+xset = ipo4xcmsSet(directory, parametersOutput, listArguments, samplebyclass)
+
+
+
+cat("\n\n")
+
+
+# ----- EXPORT -----
+
+cat("\tXSET OBJECT INFO\n")
+print(xset)
+#delete the parameters to avoid the passage to the next tool in .RData image
+
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xset","zipfile")
+save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
+
+cat("\n\n")
+
+
+cat("\tDONE\n")
+