--- a/ipo4retgroup.r	Thu Aug 03 06:00:00 2017 -0400
+++ b/ipo4retgroup.r	Mon Dec 16 05:26:42 2019 -0500
@@ -2,155 +2,66 @@
 #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 -----
+cat("\tSESSION INFO\n")
 
-# ----- 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="/")) }
+#Import the different functions
+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+source_local("lib.r")
+
+pkgs <- c("IPO","batch")
+loadAndDisplayPackages(pkgs)
 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')
+args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), 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")
 
-
-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 = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
-    singlefile_sampleName = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
+if (!is.null(args$samplebyclass)){
+  samplebyclass = args$samplebyclass; args$samplebyclass=NULL
 }
 
-# single file case
-#@TODO: need to be refactoring
-if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
-
-    cwd=getwd()
-    dir.create("raw")
-    setwd("raw")
-
-    for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPath))) {
-        if(!file.exists(singlefile_galaxyPath[singlefile_galaxyPath_i])){
-            error_message=paste("Cannot access the sample:",singlefile_sampleName[singlefile_galaxyPath_i],"located:",singlefile_galaxyPath[singlefile_galaxyPath_i],". Please, contact your administrator ... if you have one!")
-            print(error_message); stop(error_message)
-        }
-        file.symlink(singlefile_galaxyPath[singlefile_galaxyPath_i],singlefile_sampleName[singlefile_galaxyPath_i])
-    }
-
-    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")
 
+# ----- INFILE PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+options(bitmapType='cairo')
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image); args$image=NULL
+
+# Because so far CAMERA isn't compatible with the new XCMSnExp object
+if (exists("xdata")){
+    xset <- getxcmsSetObject(xdata)
+}
+
+if (!exists("xset")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata' which is provided by the tool: MSnbase readMSData")
 
 
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args)
+singlefile <- rawFilePath$singlefile
+print(singlefile)
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, NULL)
 
 
+cat("\n\n")
+
 
 # ----- MAIN PROCESSING INFO -----
 cat("\tMAIN PROCESSING INFO\n")
 
-
-ipo4retgroup(xset, directory, parametersOutput, listArguments, samplebyclass)
-
-
-
-cat("\n\n")
-
-
-# ----- EXPORT -----
-
-cat("\tEXPORTING INFO\n")
-
-#save.image(file="ipo-retcor.RData")
+ipo4retgroup(xset, directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass)
 
 cat("\n\n")