# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1418289018 -3600
# Node ID 684d2341968cfbce2e86ad7a8b88abae88a8950b
# Parent  93102202ab79f27d6783fea0d38a3819f851d20f
moved polarity parameter

diff -r 93102202ab79 -r 684d2341968c metaMS_cmd_pick_and_group.r
--- 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)
diff -r 93102202ab79 -r 684d2341968c metams_lcms_pick_and_group.xml
--- 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>