comparison xcms_merge.r @ 8:6b5504f877ff draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f

7:dca722aecb67

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

for(image in args$images) {
    load(image)
    cat(sampleNamesList$sampleNamesOrigin,"\n")
    if (!exists("xdata_merged")) {
        xdata_merged <- xdata
        singlefile_merged <- singlefile
        md5sumList_merged <- md5sumList

        error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
        print(error_message)
        stop(error_message)
    }
}
save.image()

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

8:6b5504f877ff

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

for(image in args$images) {
    load(image)
    if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*")
    cat(sampleNamesList$sampleNamesOrigin,"\n")
    if (!exists("xdata_merged")) {
        xdata_merged <- xdata
        singlefile_merged <- singlefile
        md5sumList_merged <- md5sumList

        error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
        print(error_message)
        stop(error_message)
    }
}

# 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)
cat("\n\n")