Mercurial > repos > lecorguille > xcms_export_samplemetadata
view xcms_export_samplemetadata.r @ 1:008aceb33627 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86-dirty
author | lecorguille |
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date | Tue, 09 Oct 2018 12:57:14 -0400 |
parents | e3c06320f884 |
children | 942ffa3c38b8 |
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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") source_local("lib-xcms3.x.x.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 sampleMetadata <- NULL for(image in args$images) { load(image) if (is.null(sampleMetadata)) sampleMetadata <- xdata@phenoData@data else sampleMetadata <- rbind(sampleMetadata,xdata@phenoData@data) } colnames(sampleMetadata) <- c("sample_name","class") sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name) # Create a sampleMetada file write.table(sampleMetadata,file="sampleMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)