--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA.r	Mon Apr 25 11:06:25 2016 -0400
@@ -0,0 +1,175 @@
+#!/usr/bin/env Rscript
+# CAMERA.r version="2.2.1"
+
+
+
+# ----- PACKAGE -----
+cat("\tPACKAGE INFO\n")
+
+setRepositories(graphics=F, ind=31)
+
+#pkgs=c("xcms","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","igraph","CAMERA","multtest","batch")
+for(p in pkgs) {
+  suppressPackageStartupMessages(suppressWarnings(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')
+
+cat("\n\n");
+
+
+# ----- PROCESSING INFILE -----
+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
+}
+
+if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
+  load(listArguments[["image_pos"]])
+  xaP=xa
+  listOFlistArgumentsP=listOFlistArguments
+  if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
+  
+  diffrepP=NULL
+  if (exists("diffrep")) diffrepP=diffrep
+
+  load(listArguments[["image_neg"]])
+  xaN=xa
+  listOFlistArgumentsN=listOFlistArguments
+  if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
+
+  diffrepN=NULL
+  if (exists("diffrep")) diffrepN=diffrep
+}
+
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+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
+}
+
+dataMatrixOutput = "dataMatrix.tsv"
+if (!is.null(listArguments[["dataMatrixOutput"]])){
+  dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
+}
+
+variableMetadataOutput = "variableMetadata.tsv"
+if (!is.null(listArguments[["variableMetadataOutput"]])){
+  variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
+}
+
+if (!is.null(listArguments[["new_file_path"]])){
+  new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
+}
+
+#Import the different functions
+source_local("lib.r")
+
+#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
+}
+
+# We unzip automatically the chromatograms from the zip files.
+if (thefunction %in% c("annotatediff"))  {
+  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)
+    }
+
+    #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 xset object to the list of arguments in the first position
+if (exists("xset") != 0){
+  listArguments=append(list(xset), listArguments)
+}
+
+cat("\n\n")
+
+
+
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+#change the default display settings
+pdf(file=rplotspdf, width=16, height=12)
+
+
+if (thefunction %in% c("annotatediff")) {
+  results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
+  xa=results_list[["xa"]]
+  diffrep=results_list[["diffrep"]]
+  variableMetadata=results_list[["variableMetadata"]]
+
+  cat("\n\n")
+  cat("\tXSET OBJECT INFO\n")
+  print(xa)
+}
+
+if (thefunction %in% c("combinexsAnnos")) {
+  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,listOFlistArgumentsP=listOFlistArgumentsP,listOFlistArgumentsN=listOFlistArgumentsN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
+}
+
+dev.off()
+
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
+save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
+
+cat("\n\n")
+
+cat("\tDONE\n")