Mercurial > repos > lecorguille > xcms_merge
view xcms_merge.r @ 15:58b5a4b6e1da draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:17:38 +0000 |
parents | 5bd125a3f3b0 |
children |
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#!/usr/bin/env Rscript #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") loadAndDisplayPackages(pkgs) cat("\n\n") args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects cat("\tXSET MERGING...\n") mergeXDataReturn <- mergeXData(args) xdata <- mergeXDataReturn$xdata singlefile <- mergeXDataReturn$singlefile md5sumList <- mergeXDataReturn$md5sumList sampleNamesList <- mergeXDataReturn$sampleNamesList chromTIC <- mergeXDataReturn$chromTIC chromBPI <- mergeXDataReturn$chromBPI # Create a sampleMetada file sampleNamesList <- getSampleMetadata(xdata = xdata, sampleMetadataOutput = "sampleMetadata.tsv") cat("\n\n") cat("\tXCMSnExp OBJECT INFO\n") print(pData(xdata)) print(xdata) cat("\n\n") cat("\txcmsSet OBJECT INFO\n") # Get the legacy xcmsSet object xset <- getxcmsSetObject(xdata) print(xset@phenoData) print(xset) cat("\n\n") cat("\tSAVE RData\n") #saving R data in .Rdata file to save the variables used in the present tool objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") save(list = objects2save[objects2save %in% ls()], file = "merged.RData")