Mercurial > repos > lecorguille > xcms_group

comparison xcms_group.r @ 19:c8f8d598f562 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Mon, 11 Feb 2019 06:02:39 -0500
parents 833d2c821d9c
children 6842c495da6d
comparison
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18:7a19925478e8 19:c8f8d598f562
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")
16 15
17 pkgs <- c("xcms","batch","RColorBrewer") 16 pkgs <- c("xcms","batch","RColorBrewer")
18 loadAndDisplayPackages(pkgs) 17 loadAndDisplayPackages(pkgs)
19 cat("\n\n"); 18 cat("\n\n");
20 19
82 print(groupChromPeaksParam) 81 print(groupChromPeaksParam)
83 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam) 82 xdata <- groupChromPeaks(xdata, param = groupChromPeaksParam)
84 83
85 84
86 cat("\t\tDRAW GRAPHICS\n") 85 cat("\t\tDRAW GRAPHICS\n")
87 getPlotChromPeakDensity(xdata) 86 getPlotChromPeakDensity(xdata, param = groupChromPeaksParam)
88 87
89 if (exists("intval")) { 88 if (exists("intval")) {
90 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") 89 getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv")
91 } 90 }
92 91