Mercurial > repos > lecorguille > xcms_group

comparison xcms_group.r @ 36:eddc995c6df1 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
author lecorguille
date Mon, 17 Sep 2018 08:45:13 -0400
parents 59943e24684b
children 87c082612887
comparison
equal deleted inserted replaced
35:aeba79c716b1 36:eddc995c6df1
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","RColorBrewer") 17 pkgs <- c("xcms","batch","RColorBrewer")
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 -----
83 85
84 cat("\t\tDRAW GRAPHICS\n") 86 cat("\t\tDRAW GRAPHICS\n")
85 getPlotChromPeakDensity(xdata) 87 getPlotChromPeakDensity(xdata)
86 88
87 if (exists("intval")) { 89 if (exists("intval")) {
88 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, "variableMetadata.tsv", "dataMatrix.tsv") 90 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
89 } 91 }
90 92
91 cat("\n\n") 93 cat("\n\n")
92 94
93 # ----- EXPORT ----- 95 # ----- EXPORT -----