comparison metaMS_cmd_pick_and_group.r @ 51:684d2341968c

moved polarity parameter

50:93102202ab79

## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
args.outPeakTable <- args[3]
args.xsetOut <- args[4]

## report files
args.htmlReportFile <- args[5]
args.htmlReportFile.files_path <- args[6]


if (length(args) == 7)
{
	args.outLogFile <- args[7]
	# suppress messages:
	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
	msg <- file(args.outLogFile, open="wt")
	sink(msg, type="message") 
	sink(msg, type="output")

			source(args.settings, local=tempEnv)
			message(paste(" loaded : ", args.settings))
			allSettings <- tempEnv[["customMetaMSsettings"]] 
			
			# trigger runLC: 
			LC <- runLC(files, settings = allSettings, nSlaves=20, returnXset = TRUE)
			
			# write out runLC annotation results:
			write.table(LC$PeakTable, args.outPeakTable, sep="\t", row.names=FALSE)
			
			# save xset as rdata:

51:684d2341968c

## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
args.outPeakTable <- args[3]
args.xsetOut <- args[4]

# polarity as explicit parameter: 
args.runLC_polarity <- args[5]

## report files
args.htmlReportFile <- args[6]
args.htmlReportFile.files_path <- args[7]


if (length(args) == 8)
{
	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")
	sink(msg, type="message") 
	sink(msg, type="output")

			source(args.settings, local=tempEnv)
			message(paste(" loaded : ", args.settings))
			allSettings <- tempEnv[["customMetaMSsettings"]] 
			
			# trigger runLC: 
			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)
			
			# save xset as rdata: