Mercurial > repos > lecorguille > msnbase_readmsdata
view msnbase_readmsdata.r @ 9:a874afcb71ca draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author | lecorguille |
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date | Mon, 29 Apr 2019 06:18:40 -0400 |
parents | b6ef94529e50 |
children | 0a0164b8c24d |
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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=F, quote=F, 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 <- getRawfilePathFromArguments(singlefile, zipfile, args) zipfile <- rawFilePath$zipfile singlefile <- rawFilePath$singlefile directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) # Check some character issues md5sumList <- list("origin" = getMd5sum(directory)) checkXmlStructure(directory) checkFilesCompatibilityWithXcms(directory) cat("\n\n") # ----- MAIN PROCESSING INFO ----- cat("\tMAIN PROCESSING INFO\n") cat("\t\tCOMPUTE\n") ## Get the full path to the files files <- getMSFiles(directory) 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("\t\t\tCompute and Store TIC and BPI\n") chromTIC <- chromatogram(raw_data, aggregationFun = "sum") chromBPI <- chromatogram(raw_data, aggregationFun = "max") 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")