--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_refine.r	Thu Jun 17 07:42:55 2021 +0000
@@ -0,0 +1,126 @@
+#!/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");
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+# interpretation of arguments given in command line as an R list of objects
+args <- parseCommandArgs(evaluate = FALSE)
+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$msLevel
+param_args <- list()
+
+if (args_method == "CleanPeaks") {
+  param_args$maxPeakwidth <- args$maxPeakwidth
+} else if (args_method == "FilterIntensity") {
+  param_args$threshold <- args$threshold
+  param_args$value <- args$value
+  param_args$nValues <- args$nValues
+} else if (args_method == "MergeNeighboringPeaks") {
+  param_args$expandRt <- args$expandRt
+  param_args$expandMz <- args$expandMz
+  param_args$ppm      <- args$ppm
+  param_args$minProp  <- args$minProp
+}
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args_image)
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. Such RData as this might have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+zipfile <- rawFilePath$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")
+
+xdata <- updateObject(xdata)
+
+xdata <- refineChromPeaks(xdata, param = refineChromPeaksParam)
+
+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")