Mercurial > repos > workflow4metabolomics > xcms_refine
view xcms_refine.r @ 2:090b33a9981c draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author | workflow4metabolomics |
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date | Mon, 15 Jul 2024 16:00:52 +0000 |
parents | 20f8ebc3a391 |
children |
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#!/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 = FALSE, quote = FALSE, 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")