Mercurial > repos > lecorguille > xcms_fillpeaks

comparison xcms_fillpeaks.r @ 38:a3e80894efd3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
author lecorguille
date Mon, 17 Sep 2018 08:46:47 -0400
parents e67cbb96d9e9
children a98dbb09fed1
comparison
equal deleted inserted replaced
37:9eefb022a189 38:a3e80894efd3
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){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } 13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
14 source_local("lib.r") 14 source_local("lib.r")
15 source_local("lib-xcms3.x.x.r")
15 16
16 pkgs <- c("xcms","batch") 17 pkgs <- c("xcms","batch")
17 loadAndDisplayPackages(pkgs) 18 loadAndDisplayPackages(pkgs)
18 cat("\n\n"); 19 cat("\n\n");
19 20
33 34
34 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute 35 if (!is.null(args$convertRTMinute)) convertRTMinute <- args$convertRTMinute
35 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ 36 if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ
36 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT 37 if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT
37 if (!is.null(args$intval)) intval <- args$intval 38 if (!is.null(args$intval)) intval <- args$intval
39 if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero
38 40
39 cat("\n\n") 41 cat("\n\n")
40 42
41 43
42 # ----- ARGUMENTS PROCESSING ----- 44 # ----- ARGUMENTS PROCESSING -----
79 fillChromPeaksParam <- do.call(paste0(method,"Param"), args) 81 fillChromPeaksParam <- do.call(paste0(method,"Param"), args)
80 print(fillChromPeaksParam) 82 print(fillChromPeaksParam)
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, "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 -----