Mercurial > repos > lecorguille > xcms_export_samplemetadata

comparison xcms_export_samplemetadata.r @ 10:cdab04a1d1d7 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:14:35 +0000
parents 94eb263cfab4
children
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9:94eb263cfab4 10:cdab04a1d1d7
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 #Import the different functions 3 #Import the different functions
4 source_local <- function(fname) { 4 source_local <- function(fname) {
5 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) 5 argv <- commandArgs(trailingOnly = FALSE)
6 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
7 source(paste(base_dir, fname, sep = "/"))
6 } 8 }
7 source_local("lib.r") 9 source_local("lib.r")
8 10
9 pkgs <- c("xcms", "batch") 11 pkgs <- c("xcms", "batch")
10 loadAndDisplayPackages(pkgs) 12 loadAndDisplayPackages(pkgs)
11 cat("\n\n"); 13 cat("\n\n")
12 14
13 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects 15 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
14 16
15 17
16 sampleMetadata <- NULL 18 sampleMetadata <- NULL
17 for (image in args$images) { 19 for (image in args$images) {
18 load(image) 20 load(image)
19 if (exists("raw_data")) xdata <- raw_data 21 if (exists("raw_data")) xdata <- raw_data
20 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.*") 22 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.*")
21 if (is.null(sampleMetadata)) 23 if (is.null(sampleMetadata))
22 sampleMetadata <- xdata@phenoData@data 24 sampleMetadata <- xdata@phenoData@data
23 else 25 else
24 sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data) 26 sampleMetadata <- rbind(sampleMetadata, xdata@phenoData@data)
25 } 27 }
26 colnames(sampleMetadata) <- c("sample_name", "class") 28 colnames(sampleMetadata) <- c("sample_name", "class")
27 sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name) 29 sampleMetadata$sample_name <- make.names(sampleMetadata$sample_name)
28 30
29 # Create a sampleMetada file 31 # Create a sampleMetada file