comparison xcms_merge.r @ 10:47e953d9da82 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

9:35b9bb3205d8

cat("\tXSET MERGING...\n")

for(image in args$images) {
    load(image)

    # 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)
    
    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.*")
    cat(sampleNamesList$sampleNamesOrigin,"\n")
    if (!exists("xdata_merged")) {
        xdata_merged <- xdata
        singlefile_merged <- singlefile

}

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

# Get the legacy xcmsSet object
xset <- getxcmsSetObject(xdata)

cat("\n\n")


# -- TIC --
cat("\t\tGET TIC GRAPH\n")
#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method
getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf")
getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf")

cat("\n\n")

cat("\tXCMSnExp OBJECT INFO\n")
print(pData(xdata))
print(xdata)

10:47e953d9da82

cat("\tXSET MERGING...\n")

for(image in args$images) {
    load(image)
    print(args)
    # Handle infiles
    if (!exists("singlefile")) singlefile <- NULL
    if (!exists("zipfile")) zipfile <- NULL
    rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
    zipfile <- rawFilePath$zipfile
    singlefile <- rawFilePath$singlefile
    directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)

    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.*")
    cat(sampleNamesList$sampleNamesOrigin,"\n")
    if (!exists("xdata_merged")) {
        xdata_merged <- xdata
        singlefile_merged <- singlefile

}

# Create a sampleMetada file
sampleNamesList <- getSampleMetadata(xdata=xdata, sampleMetadataOutput="sampleMetadata.tsv")

cat("\n\n")

cat("\tXCMSnExp OBJECT INFO\n")
print(pData(xdata))
print(xdata)