comparison xcms_fillpeaks.r @ 26:bb9ee352fce0 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
author workflow4metabolomics
date Mon, 11 Sep 2023 09:15:33 +0000
parents 26d77e9ceb49
children
comparison
equal deleted inserted replaced
25:26d77e9ceb49 26:bb9ee352fce0
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") 20 pkgs <- c("xcms", "batch")
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 xdata <- updateObject(xdata) 81 xdata <- updateObject(xdata)
80 register(SerialParam()) 82 register(SerialParam())
81 xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam) 83 xdata <- fillChromPeaks(xdata, param = fillChromPeaksParam)
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 -----