Mercurial > repos > lecorguille > xcms_group

comparison xcms_group.r @ 28:2b676d5eb848 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 09:16:31 +0000
parents d45a786cbc40
children
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27:d45a786cbc40 28:2b676d5eb848
9 # ----- PACKAGE ----- 9 # ----- PACKAGE -----
10 cat("\tSESSION INFO\n") 10 cat("\tSESSION INFO\n")
11 11
12 #Import the different functions 12 #Import the different functions
13 source_local <- function(fname) { 13 source_local <- function(fname) {
14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) 14 argv <- commandArgs(trailingOnly = FALSE)
15 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
16 source(paste(base_dir, fname, sep = "/"))
15 } 17 }
16 source_local("lib.r") 18 source_local("lib.r")
17 19
18 pkgs <- c("xcms", "batch", "RColorBrewer") 20 pkgs <- c("xcms", "batch", "RColorBrewer")
19 loadAndDisplayPackages(pkgs) 21 loadAndDisplayPackages(pkgs)
20 cat("\n\n"); 22 cat("\n\n")
21 23
22 24
23 # ----- ARGUMENTS ----- 25 # ----- ARGUMENTS -----
24 cat("\tARGUMENTS INFO\n") 26 cat("\tARGUMENTS INFO\n")
25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects 27 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") 28 write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t")
27 29
28 cat("\n\n") 30 cat("\n\n")
29 31
30 # ----- PROCESSING INFILE ----- 32 # ----- PROCESSING INFILE -----
31 cat("\tARGUMENTS PROCESSING INFO\n") 33 cat("\tARGUMENTS PROCESSING INFO\n")
79 81
80 cat("\t\tDRAW GRAPHICS\n") 82 cat("\t\tDRAW GRAPHICS\n")
81 getPlotChromPeakDensity(xdata, param = groupChromPeaksParam) 83 getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
82 84
83 if (exists("intval")) { 85 if (exists("intval")) {
84 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") 86 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
85 } 87 }
86 88
87 cat("\n\n") 89 cat("\n\n")
88 90
89 # ----- EXPORT ----- 91 # ----- EXPORT -----