--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_group.r	Tue Sep 18 16:11:06 2018 -0400
@@ -0,0 +1,114 @@
+#!/usr/bin/env Rscript
+
+# ----- LOG FILE -----
+log_file=file("log.txt", open = "wt")
+sink(log_file)
+sink(log_file, type = "output")
+
+
+# ----- PACKAGE -----
+cat("\tSESSION INFO\n")
+
+#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")
+source_local("lib-xcms3.x.x.r")
+
+pkgs <- c("xcms","batch","RColorBrewer")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
+
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+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")
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the specific parameters
+method <- args$method
+
+if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
+if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
+if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
+if (!is.null(args$intval)) intval <- args$intval
+if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
+
+# Check some character issues
+md5sumList <- list("origin" = getMd5sum(directory))
+checkXmlStructure(directory)
+checkFilesCompatibilityWithXcms(directory)
+
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+
+cat("\t\t\tPerform the correspondence\n")
+args$sampleGroups = xdata$sample_group
+
+# clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or method ...
+args <- args[names(args) %in% slotNames(do.call(paste0(method,"Param"), list(sampleGroups=c(1,2))))]
+
+groupChromPeaksParam <- do.call(paste0(method,"Param"), args)
+print(groupChromPeaksParam)
+xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
+
+
+cat("\t\tDRAW GRAPHICS\n")
+getPlotChromPeakDensity(xdata)
+
+if (exists("intval")) {
+    getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
+}
+
+cat("\n\n")
+
+# ----- EXPORT -----
+
+cat("\tXCMSnExp OBJECT INFO\n")
+print(xdata)
+cat("\n\n")
+
+cat("\txcmsSet OBJECT INFO\n")
+# Get the legacy xcmsSet object
+xset <- getxcmsSetObject(xdata)
+print(xset)
+cat("\n\n")
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList", "chromTIC", "chromBPI", "chromTIC_adjusted", "chromBPI_adjusted")
+save(list=objects2save[objects2save %in% ls()], file="group.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")