Mercurial > repos > pieterlukasse > prims_metabolomics

comparison metaMS_cmd_pick_and_group.r @ 51:684d2341968c

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moved polarity parameter
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 10:10:18 +0100
parents f772a5caa86a
children
comparison
equal deleted inserted replaced
50:93102202ab79 51:684d2341968c
9 9
10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt" 10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
11 args.outPeakTable <- args[3] 11 args.outPeakTable <- args[3]
12 args.xsetOut <- args[4] 12 args.xsetOut <- args[4]
13 13
14 # polarity as explicit parameter:
15 args.runLC_polarity <- args[5]
16
14 ## report files 17 ## report files
15 args.htmlReportFile <- args[5] 18 args.htmlReportFile <- args[6]
16 args.htmlReportFile.files_path <- args[6] 19 args.htmlReportFile.files_path <- args[7]
17 20
18 21
19 if (length(args) == 7) 22 if (length(args) == 8)
20 { 23 {
21 args.outLogFile <- args[7] 24 args.outLogFile <- args[8]
22 # suppress messages: 25 # suppress messages:
23 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888 26 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
24 msg <- file(args.outLogFile, open="wt") 27 msg <- file(args.outLogFile, open="wt")
25 sink(msg, type="message") 28 sink(msg, type="message")
26 sink(msg, type="output") 29 sink(msg, type="output")
42 source(args.settings, local=tempEnv) 45 source(args.settings, local=tempEnv)
43 message(paste(" loaded : ", args.settings)) 46 message(paste(" loaded : ", args.settings))
44 allSettings <- tempEnv[["customMetaMSsettings"]] 47 allSettings <- tempEnv[["customMetaMSsettings"]]
45 48
46 # trigger runLC: 49 # trigger runLC:
47 LC <- runLC(files, settings = allSettings, nSlaves=20, returnXset = TRUE) 50 LC <- runLC(files, settings = allSettings, polarity=args.runLC_polarity, nSlaves=20, returnXset = TRUE)
48 51
49 # write out runLC annotation results: 52 # write out runLC annotation results:
50 write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE) 53 write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
51 54
52 # save xset as rdata: 55 # save xset as rdata: