--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms.r	Fri Apr 08 10:38:52 2016 -0400
@@ -0,0 +1,246 @@
+#!/usr/bin/env Rscript
+# xcms.r version="2.2.0"
+#Authors ABIMS TEAM
+#BPC Addition from Y.guitton
+
+
+# ----- LOG FILE -----
+log_file=file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+cat("\tPACKAGE INFO\n")
+#pkgs=c("xcms","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch")
+for(pkg in pkgs) {
+  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")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+if (!is.null(listArguments[["image"]])){
+  load(listArguments[["image"]]); listArguments[["image"]]=NULL
+}
+
+#Import the different functions
+source_local("lib.r")
+
+cat("\n\n")
+
+#Import the different functions
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+# Save arguments to generate a report
+if (!exists("listOFlistArguments")) listOFlistArguments=list()
+listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
+
+
+#saving the commun parameters
+thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments
+
+xsetRdataOutput = paste(thefunction,"RData",sep=".")
+if (!is.null(listArguments[["xsetRdataOutput"]])){
+  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
+}
+
+rplotspdf = "Rplots.pdf"
+if (!is.null(listArguments[["rplotspdf"]])){
+  rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
+}
+
+sampleMetadataOutput = "sampleMetadata.tsv"
+if (!is.null(listArguments[["sampleMetadataOutput"]])){
+  sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL
+}
+
+
+
+
+if (thefunction %in% c("xcmsSet","retcor")) {
+  ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL
+  bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=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[["library"]])){
+  directory=listArguments[["library"]]; listArguments[["library"]]=NULL
+  if(!file.exists(directory)){
+    error_message=paste("Cannot access the directory:",directory,". Please verify if the directory exists or not.")
+    print(error_message)
+    stop(error_message)
+  }
+}
+
+# We unzip automatically the chromatograms from the zip files.
+if (thefunction %in% c("xcmsSet","retcor","fillPeaks"))  {
+  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"]
+
+
+    #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")
+
+    # 
+    md5sumList=list("origin"=getMd5sum(directory))
+
+    # Check and fix if there are non ASCII characters. If so, they will be removed from the *mzXML mzML files.
+    # Remove because can create issue with some clean files
+    #@TODO: fix me
+    #if (deleteXmlBadCharacters(directory)) {
+    #  md5sumList=list("removalBadCharacters"=getMd5sum(directory))
+    #}
+
+  }
+}
+
+#addition of the directory to the list of arguments in the first position
+if (thefunction == "xcmsSet") {
+  checkXmlStructure(directory)
+  checkFilesCompatibilityWithXcms(directory)
+  listArguments=append(directory, listArguments)
+}
+
+
+#addition of xset object to the list of arguments in the first position
+if (exists("xset")){
+  listArguments=append(list(xset), listArguments)
+}
+
+cat("\n\n")
+
+
+
+
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+#Verification of a group step before doing the fillpeaks job.
+
+if (thefunction == "fillPeaks") {
+  res=try(is.null(groupnames(xset)))
+  if (class(res) == "try-error"){
+    error<-geterrmessage()
+    write(error, stderr())
+    stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step")
+  }
+
+}
+
+#change the default display settings
+#dev.new(file="Rplots.pdf", width=16, height=12)
+pdf(file=rplotspdf, width=16, height=12)
+if (thefunction == "group") {
+  par(mfrow=c(2,2))
+}
+#else if (thefunction == "retcor") {
+#try to change the legend display
+#     par(xpd=NA)
+#     par(xpd=T, mar=par()$mar+c(0,0,0,4))
+#}
+
+
+#execution of the function "thefunction" with the parameters given in "listArguments"
+xset = do.call(thefunction, listArguments)
+
+
+cat("\n\n")
+
+dev.off() #dev.new(file="Rplots.pdf", width=16, height=12)
+
+if (thefunction  == "xcmsSet") {
+
+  #transform the files absolute pathways into relative pathways
+  xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
+
+  if(exists("zipfile") && (zipfile!="")) {
+    
+    #Modify the samples names (erase the path)
+    for(i in 1:length(sampnames(xset))){
+
+      sample_name=unlist(strsplit(sampnames(xset)[i], "/"))
+      sample_name=sample_name[length(sample_name)]
+      sample_name= unlist(strsplit(sample_name,"[.]"))[1]
+      sampnames(xset)[i]=sample_name
+
+    }
+
+  }
+
+}
+
+# -- TIC --
+if (thefunction == "xcmsSet") {
+  sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput)
+  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw")
+  getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf)
+} else if (thefunction == "retcor") {
+  getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected")
+  getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf)
+}
+
+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","listOFlistArguments","md5sumList","sampleNamesList")
+save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
+
+cat("\n\n")
+
+
+cat("\tDONE\n")
+