--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_refine.r	Fri Feb 12 18:05:29 2021 +0000
@@ -0,0 +1,169 @@
+#!/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")
+
+pkgs <- c("xcms","batch","RColorBrewer")
+loadAndDisplayPackages(pkgs)
+cat("\n\n");
+
+# ----- EXPLORE NAMESPACE -----
+# cat("\tXCMS NAMESPACE INFO\n")
+# ls(asNamespace("xcms"))
+
+# ----- 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
+args_method  <- args$method
+args_image   <- args$image
+args_msLevel <- args$msLevel
+#args[c('method','image','msLevel')] <- NULL
+param_args <- list()
+
+if ( args_method == "CleanPeaks" ) {
+  param_args$maxPeakwidth <- as.numeric(args$maxPeakwidth)
+  if (is.na(as.numeric(param_args$maxPeakwidth))) stop("\n\nERROR: The maxPeakwidth argument cannot be coerced to a numeric value.")
+} else if ( args_method == "FilterIntensity" ) {
+  param_args$threshold <- as.numeric(args$threshold)
+  if (is.na(as.numeric(param_args$threshold))) stop("\n\nERROR: The threshold argument cannot be coerced to a numeric value.")
+  param_args$nValues <- as.numeric(args$nValues)
+  if (is.na(as.numeric(param_args$nValues))) stop("\n\nERROR: The nValues argument cannot be coerced to a numeric value.")
+  if (as.integer(param_args$nValues) != param_args$nValues) stop("\n\nERROR: The nValues argument is not an integer value.")
+  param_args$value <- args$value
+} else if ( args_method == "MergeNeighboringPeaks" ) {
+  if (is.na(as.numeric(args$expandRt))) stop("\n\nERROR: The expandRt argument cannot be coerced to a numeric value.")
+  if (is.na(as.numeric(args$expandMz))) stop("\n\nERROR: The expandMz argument cannot be coerced to a numeric value.")
+  if (is.na(as.numeric(args$ppm))) stop("\n\nERROR: The ppm argument cannot be coerced to a numeric value.")
+  if (is.na(as.numeric(args$minProp))) stop("\n\nERROR: The minProp argument cannot be coerced to a numeric value.")
+  param_args$expandRt <- args$expandRt
+  param_args$expandMz <- args$expandMz
+  param_args$ppm      <- args$ppm
+  param_args$minProp  <- args$minProp
+}
+
+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'. Such RData as this might have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tPREPARE PARAMETERS\n\n")
+
+if ( args_method == "CleanPeaks" ) {
+  refineChromPeaksParam <- CleanPeaksParam(maxPeakwidth = param_args$maxPeakwidth)
+} else if ( args_method == "FilterIntensity" ) {
+  refineChromPeaksParam <- FilterIntensityParam(
+    threshold = param_args$threshold,
+    nValues = param_args$nValues,
+    value = param_args$value
+  )
+} else if ( args_method == "MergeNeighboringPeaks" ) {
+  refineChromPeaksParam <- MergeNeighboringPeaksParam(
+    expandRt = param_args$expandRt,
+    expandMz = param_args$expandMz,
+    ppm = param_args$ppm,
+    minProp = param_args$minProp
+  )
+}
+
+cat(str(refineChromPeaksParam))
+
+cat("\n\n\t\tCOMPUTE\n")
+
+# cat("\t\t\tACE DEBUG show the xdata\n")
+# cat(str(xdata))
+# cat("\n\t\t\tACE DEBUG (end show the xdata)\n")
+
+# cat("\t\t\tACE DEBUG show updateObject(xdata)\n")
+xdata <- updateObject(xdata)
+# cat(str(xdata))
+# cat("\n\t\t\tACE DEBUG (end show updateObject(xdata))\n")
+# 
+# cat("\t\t\tACE DEBUG show the param_args\n")
+# cat(str(param_args))
+# cat("\n\t\t\tACE DEBUG (end show the param_args)\n")
+# 
+# cat("\t\t\tACE DEBUG show the refineChromPeaksParam\n")
+# cat(str(refineChromPeaksParam))
+# cat("\n\t\t\tACE DEBUG (end show the refineChromPeaksParam)\n")
+# 
+# cat("\t\t\tACE DEBUG show the slotNames\n")
+# cat(str(slotNames(refineChromPeaksParam)))
+# cat("\n\t\t\tACE DEBUG (end show the slotNames)\n")
+
+# # clear the arguement list to remove unexpected key/value as singlefile_galaxyPath or args_method ...
+# param_args <- param_args[names(param_args) %in% slotNames(do.call(paste0(args_method,"Param"), param_args))]
+#
+# refineChromPeaksParam <- do.call(paste0(args_method,"Param"), param_args)
+# print(refineChromPeaksParam)
+
+# cat("\t\t\tACE DEBUG invoke refineChromPeaks\n")
+xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
+# cat("\t\t\tACE DEBUG returned from refineChromPeaks\n")
+#
+#
+# cat("\t\tDRAW GRAPHICS\n")
+# getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
+#
+# 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")
+save(list=objects2save[objects2save %in% ls()], file="xcmsSet.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")