comparison lib.r @ 17:b6b62413936f draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989

16:34fe699200ce

    variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
    dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)

    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)

}

    cat("Creating the sampleMetadata file...\n")

    #Create the sampleMetada dataframe
    sampleMetadata <- xdata@phenoData@data
    rownames(sampleMetadata) <- NULL
    colnames(sampleMetadata) <-  c("sampleMetadata", "class")

    sampleNamesOrigin <- sampleMetadata$sampleMetadata
    sampleNamesMakeNames <- make.names(sampleNamesOrigin)

    if (any(duplicated(sampleNamesMakeNames))) {
        write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
        for (sampleName in sampleNamesOrigin) {

        for (sampleName in sampleNamesOrigin) {
            cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
        }
    }

    sampleMetadata$sampleMetadata <- sampleNamesMakeNames


    #For each sample file, the following actions are done
    for (fileIdx in 1:length(fileNames(xdata))) {
        #Check if the file is in the CDF format

17:b6b62413936f

    variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
    variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
    dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)

    # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
    variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")

    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)

}

    cat("Creating the sampleMetadata file...\n")

    #Create the sampleMetada dataframe
    sampleMetadata <- xdata@phenoData@data
    rownames(sampleMetadata) <- NULL
    colnames(sampleMetadata) <-  c("sample_name", "class")

    sampleNamesOrigin <- sampleMetadata$sample_name
    sampleNamesMakeNames <- make.names(sampleNamesOrigin)

    if (any(duplicated(sampleNamesMakeNames))) {
        write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
        for (sampleName in sampleNamesOrigin) {

        for (sampleName in sampleNamesOrigin) {
            cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
        }
    }

    sampleMetadata$sample_name <- sampleNamesMakeNames


    #For each sample file, the following actions are done
    for (fileIdx in 1:length(fileNames(xdata))) {
        #Check if the file is in the CDF format