Mercurial > repos > lecorguille > xcms_export_samplemetadata
diff xcms_export_samplemetadata.r @ 10:cdab04a1d1d7 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author | workflow4metabolomics |
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date | Mon, 11 Sep 2023 09:14:35 +0000 |
parents | 94eb263cfab4 |
children |
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--- a/xcms_export_samplemetadata.r Wed Apr 07 09:53:54 2021 +0000 +++ b/xcms_export_samplemetadata.r Mon Sep 11 09:14:35 2023 +0000 @@ -2,26 +2,28 @@ #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 = "/")) + 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"); +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$images) { - load(image) - if (exists("raw_data")) xdata <- raw_data - if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") - if (is.null(sampleMetadata)) - sampleMetadata <- xdata@phenoData@data - else - sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) + load(image) + if (exists("raw_data")) xdata <- raw_data + if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") + if (is.null(sampleMetadata)) + sampleMetadata <- xdata@phenoData@data + else + sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) } colnames(sampleMetadata) <- c("sample_name", "class") sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name)