Mercurial > repos > lecorguille > msnbase_readmsdata
view msnbase_readmsdata.r @ 15:7faf9b2d83f6 draft
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:24:51 +0000 |
parents | 11ab2081bd4a |
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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("MSnbase", "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") cat("\n\n") # ----- INFILE PROCESSING ----- cat("\tINFILE PROCESSING INFO\n") # Handle infiles if (!exists("singlefile")) singlefile <- NULL if (!exists("zipfile")) zipfile <- NULL rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile files <- rawFilePath$files md5sumList <- list("origin" = getMd5sum(files)) cat("\n\n") # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") cat("\t\tCOMPUTE\n") cat("\t\t\tCreate a phenodata data.frame\n") s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x), "/")), n = 1)) s_name <- tools::file_path_sans_ext(basename(files)) pd <- data.frame(sample_name = s_name, sample_group = s_groups, stringsAsFactors = FALSE) print(pd) cat("\t\t\tLoad Raw Data\n") raw_data <- readMSData(files = files, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk") # Transform the files absolute pathways into relative pathways raw_data@processingData@files <- sub(paste(getwd(), "/", sep = ""), "", raw_data@processingData@files) # Create a sampleMetada file sampleNamesList <- getSampleMetadata(xdata = raw_data, sampleMetadataOutput = "sampleMetadata.tsv") cat("\n\n") # ----- EXPORT ----- cat("\tMSnExp OBJECT INFO\n") print(raw_data) cat("\t\tphenoData\n") print(raw_data@phenoData@data) cat("\n\n") #saving R data in .Rdata file to save the variables used in the present tool objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") save(list = objects2save[objects2save %in% ls()], file = "readmsdata.RData") cat("\tDONE\n")