Mercurial > repos > lecorguille > ipo
view ipo4xcmsSet.r @ 2:8e5f667359cb draft default tip
planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 22:37:32 +0000 |
parents | ae8de756dfcf |
children |
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#!/usr/bin/env Rscript # Authors Gildas Le Corguille and Yann Guitton # ----- 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("IPO", "batch") 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") options(bitmapType = "cairo") samplebyclass <- 2 if (!is.null(args$samplebyclass)) { samplebyclass <- args$samplebyclass args$samplebyclass <- NULL } # ----- INFILE PROCESSING ----- cat("\tINFILE PROCESSING INFO\n") # Handle infiles if (!exists("singlefile")) singlefile <- NULL rawFilePath <- getRawfilePathFromArguments(singlefile, NULL, args) singlefile <- rawFilePath$singlefile directory <- retrieveRawfileInWD(singlefile, NULL) # Check some character issues checkXmlStructure(directory) cat("\n\n") # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") xset <- ipo4xcmsSet(directory, "IPO_parameters4xcmsSet.tsv", args, samplebyclass) cat("\n\n") # ----- EXPORT ----- cat("\tXSET OBJECT INFO\n") print(xset) # delete the parameters to avoid the passage to the next tool in .RData image # saving R data in .Rdata file to save the variables used in the present tool objects2save <- c("xset", "singlefile") save(list = objects2save[objects2save %in% ls()], file = "ipo4xcmsSet.RData") cat("\n\n") cat("\tDONE\n")