Mercurial > repos > lecorguille > xcms_merge

comparison xcms_merge.r @ 17:ae28a753a6f8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:45:41 +0000
parents 58b5a4b6e1da
children
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16:6d475a389abc 17:ae28a753a6f8
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) 5 argv <- commandArgs(trailingOnly = FALSE)
6 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 6 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
7 source(paste(base_dir, fname, sep = "/")) 7 source(paste(base_dir, fname, sep = "/"))
8 } 8 }
9 source_local("lib.r") 9 source_local("lib.r")
10 10
11 pkgs <- c("xcms", "batch") 11 pkgs <- c("xcms", "batch")
12 loadAndDisplayPackages(pkgs) 12 loadAndDisplayPackages(pkgs)
13 cat("\n\n") 13 cat("\n\n")
14 14
15 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
16 16
17 17
18 cat("\tXSET MERGING...\n") 18 cat("\tXSET MERGING...\n")
19 19
20 mergeXDataReturn <- mergeXData(args) 20 mergeXDataReturn <- mergeXData(args)
41 print(xset@phenoData) 41 print(xset@phenoData)
42 print(xset) 42 print(xset)
43 cat("\n\n") 43 cat("\n\n")
44 44
45 cat("\tSAVE RData\n") 45 cat("\tSAVE RData\n")
46 #saving R data in .Rdata file to save the variables used in the present tool 46 # saving R data in .Rdata file to save the variables used in the present tool
47 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") 47 objects2save <- c("xdata", "zipfile", "singlefile", "md5sumList", "sampleNamesList") # , "chromTIC", "chromBPI")
48 save(list = objects2save[objects2save %in% ls()], file = "merged.RData") 48 save(list = objects2save[objects2save %in% ls()], file = "merged.RData")