diff xcms_retcor.r @ 27:8242376d9f35 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_retcor.r	Thu Mar 14 15:35:44 2024 +0000
@@ -0,0 +1,107 @@
+#!/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")
+args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
+
+cat("\n\n")
+
+# ----- PROCESSING INFILE -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+#saving the specific parameters
+method <- args$method
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+load(args$image)
+args$image <- NULL
+if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
+
+# Handle infiles
+if (!exists("singlefile")) singlefile <- NULL
+if (!exists("zipfile")) zipfile <- NULL
+rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args)
+zipfile <- rawFilePath$zipfile
+singlefile <- rawFilePath$singlefile
+
+cat("\n\n")
+
+
+# ----- MAIN PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+
+cat("\t\tCOMPUTE\n")
+
+cat("\t\t\tAlignment/Retention Time correction\n")
+# 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()))]
+
+adjustRtimeParam <- do.call(paste0(method, "Param"), args)
+print(adjustRtimeParam)
+
+if (hasAdjustedRtime(xdata)) {
+  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+  cat("Replace raw retention times with adjusted retention times.\n")
+  xdata <- applyAdjustedRtime(xdata)
+}
+xdata <- adjustRtime(xdata, param = adjustRtimeParam)
+
+cat("\n\n")
+
+
+# -- TIC --
+cat("\t\tDRAW GRAPHICS\n")
+getPlotAdjustedRtime(xdata)
+
+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 = "retcor.RData")
+
+cat("\n\n")
+
+
+cat("\tDONE\n")