Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 51:684d2341968c
moved polarity parameter
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 11 Dec 2014 10:10:18 +0100 |
| parents | 93102202ab79 |
| children | 5b1adc49700d |
| files | metaMS_cmd_pick_and_group.r metams_lcms_pick_and_group.xml |
| diffstat | 2 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- a/metaMS_cmd_pick_and_group.r Wed Dec 10 22:04:33 2014 +0100 +++ b/metaMS_cmd_pick_and_group.r Thu Dec 11 10:10:18 2014 +0100 @@ -11,14 +11,17 @@ args.outPeakTable <- args[3] args.xsetOut <- args[4] +# polarity as explicit parameter: +args.runLC_polarity <- args[5] + ## report files -args.htmlReportFile <- args[5] -args.htmlReportFile.files_path <- args[6] +args.htmlReportFile <- args[6] +args.htmlReportFile.files_path <- args[7] -if (length(args) == 7) +if (length(args) == 8) { - args.outLogFile <- args[7] + args.outLogFile <- args[8] # suppress messages: # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 msg <- file(args.outLogFile, open="wt") @@ -44,7 +47,7 @@ allSettings <- tempEnv[["customMetaMSsettings"]] # trigger runLC: - LC <- runLC(files, settings = allSettings, nSlaves=20, returnXset = TRUE) + LC <- runLC(files, settings = allSettings, polarity=args.runLC_polarity, nSlaves=20, returnXset = TRUE) # write out runLC annotation results: write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
--- a/metams_lcms_pick_and_group.xml Wed Dec 10 22:04:33 2014 +0100 +++ b/metams_lcms_pick_and_group.xml Thu Dec 11 10:10:18 2014 +0100 @@ -9,6 +9,7 @@ $customMetaMSsettings $outputFile $xsetOut + $findAdducts_polarity $htmlReportFile $htmlReportFile.files_path $outputLog @@ -245,7 +246,6 @@ maxcharge= ${findIsotopes_maxcharge}, maxiso= ${findIsotopes_maxiso}, minfrac= ${findIsotopes_minfrac}, - polarity= "${findAdducts_polarity}", multiplier= ${findAdducts_multiplier} ))</configfile>