Mercurial > repos > lecorguille > msnbase_readmsdata
diff msnbase_readmsdata.r @ 0:728ebc7ae7dd draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:04:51 -0400 |
parents | |
children | 2a69f9923a70 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msnbase_readmsdata.r Tue Sep 18 16:04:51 2018 -0400 @@ -0,0 +1,99 @@ +#!/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") +source_local("lib-xcms3.x.x.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")