Mercurial > repos > lecorguille > xcms_export_samplemetadata
view xcms_export_samplemetadata.r @ 7:f39cd33a73a6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author | lecorguille |
---|---|
date | Mon, 29 Apr 2019 06:32:48 -0400 |
parents | 8c62030a1136 |
children | 94eb263cfab4 |
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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 sampleMetadata <- NULL for(image in args$images) { load(image) if (exists("raw_data")) xdata <- raw_data if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") if (is.null(sampleMetadata)) sampleMetadata <- xdata@phenoData@data else sampleMetadata <- rbind(sampleMetadata,xdata@phenoData@data) } colnames(sampleMetadata) <- c("sample_name","class") sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name) # Create a sampleMetada file write.table(sampleMetadata,file="sampleMetadata.tsv", sep="\t", row.names=FALSE, quote=FALSE)