Mercurial > repos > lecorguille > xcms_group
diff xcms_group.r @ 36:eddc995c6df1 draft
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 |
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--- a/xcms_group.r Wed Sep 05 05:58:38 2018 -0400 +++ b/xcms_group.r Mon Sep 17 08:45:13 2018 -0400 @@ -12,6 +12,7 @@ #Import the different functions source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("lib.r") +source_local("lib-xcms3.x.x.r") pkgs <- c("xcms","batch","RColorBrewer") loadAndDisplayPackages(pkgs) @@ -35,6 +36,7 @@ if (!is.null(args$numDigitsMZ)) numDigitsMZ <- args$numDigitsMZ if (!is.null(args$numDigitsRT)) numDigitsRT <- args$numDigitsRT if (!is.null(args$intval)) intval <- args$intval +if (!is.null(args$naTOzero)) naTOzero <- args$naTOzero cat("\n\n") @@ -85,7 +87,7 @@ getPlotChromPeakDensity(xdata) if (exists("intval")) { - getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, "variableMetadata.tsv", "dataMatrix.tsv") + getPeaklistW4M(xdata, intval, convertRTMinute, numDigitsMZ, numDigitsRT, naTOzero, "variableMetadata.tsv", "dataMatrix.tsv") } cat("\n\n")