comparison xcms_plot_chromatogram.r @ 2:e6fdadaf039e draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

1:86ff4497b871

cat("\n\n")

# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

#saving the specific parameters
method <- args$method; args$method <- NULL

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

#image is an .RData file necessary to use xset variable given by previous tools
load(args$image); args$image=NULL
if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")

# Handle infiles
if (!exists("singlefile")) singlefile <- NULL
if (!exists("zipfile")) zipfile <- NULL
rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
zipfile <- rawFilePath$zipfile
singlefile <- rawFilePath$singlefile
args <- rawFilePath$args
directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)


cat("\n\n")


# ----- MAIN PROCESSING INFO -----
cat("\tMAIN PROCESSING INFO\n")


cat("\t\tDRAW GRAPHICS\n")

#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
getPlotTICs(xdata, pdfname="TICs.pdf")
getPlotBPIs(xdata, pdfname="BPIs.pdf")

cat("\n\n")

2:e6fdadaf039e

cat("\n\n")

# ----- PROCESSING INFILE -----
cat("\tARGUMENTS PROCESSING INFO\n")

cat("\n\n")


# ----- ARGUMENTS PROCESSING -----
cat("\tINFILE PROCESSING INFO\n")

mergeXDataReturn <- mergeXData(args)
xdata <- mergeXDataReturn$xdata
singlefile <- mergeXDataReturn$singlefile
md5sumList <- mergeXDataReturn$md5sumList
sampleNamesList <- mergeXDataReturn$sampleNamesList

cat("\n\n")


# ----- MAIN PROCESSING INFO -----
cat("\tMAIN PROCESSING INFO\n")


cat("\t\tDRAW GRAPHICS\n")

getPlotTICs(xdata, pdfname="TICs.pdf")
getPlotBPIs(xdata, pdfname="BPIs.pdf")

cat("\n\n")