Mercurial > repos > pieterlukasse > prims_metabolomics2

## read args:
args <- commandArgs(TRUE)
## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
args.dataZip <- args[1]
args.zipExtrDir <- sub("\\.","_",paste(args[1],"dir", sep=""))
dir.create(file.path(args.zipExtrDir), showWarnings = FALSE, recursive = TRUE)
## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
args.settings <- args[2]

## 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")
}

cat("\nSettings used===============:\n")
cat(readChar(args.settings, 1e5))


tryCatch(
        {
	        library(metaMS)

			## load the data files from a zip file
			files <- unzip(args.dataZip, exdir=args.zipExtrDir)

			## load settings "script" into "customMetaMSsettings"
			tempEnv <- new.env()
			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:
			xsAnnotatePreparedData <- LC$xset
			saveRDS(xsAnnotatePreparedData, file=args.xsetOut)

			message("\nGenerating report.........")
			# report
			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
			html <- "<html><body><h1>Info on alignment quality </h1>"
			# TODO add (nr and mass error) and group size

			message("\nPlotting figures... ")
			figureName <- paste(args.htmlReportFile.files_path, "/figure_retcor.png", sep="")
			html <- paste(html,"<img src='figure_retcor.png' /><br/>", sep="")
			png( figureName, type="cairo", width=1100,height=600 )
			retcor(LC$xset@xcmsSet, method="peakgroups", plottype = "mdevden")
			html <- paste(html,"<a>*NB: retention time correction plot based on 'peakgroups' option with default settings. This is not the plot matching the exact settings used in the run,
									but just intended to give a rough estimate of the retention time shifts present in the data. A more accurate plot will be available once
                                    this option is added in metaMS API. </a><br/>", sep="")
			devname = dev.off()


			gt <- groups(LC$xset@xcmsSet)
			groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)

			html <- paste(html,"</body><html>")
			message("finished generating report")
			write(html,file=args.htmlReportFile)
			# unlink(args.htmlReportFile)
			cat("\nWarnings================:\n")
			str( warnings() )
		},
        error=function(cond) {
            sink(NULL, type="message") # default setting
			sink(stderr(), type="output")
            message("\nERROR: ===========\n")
            print(cond)
        }
    )
author	pieter.lukasse@wur.nl
date	Thu, 19 Mar 2015 12:22:23 +0100
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