comparison lib.r @ 27:30410a052ab3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

26:dcca50c5e1cb

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

#@author Y. Guitton
getBPC <- function(file,rtcor=NULL, ...) {
    object <- xcmsRaw(file)
    sel <- profRange(object, ...)
    cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))

            rtcor <- xcmsSet@rt$corrected[[j]]
        else
            rtcor <- NULL

        TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
        # TIC[[j]][,1]<-rtcor
    }

    for (i in 1:N) {
        if (!is.null(xcmsSet) && rt == "corrected")
            rtcor <- xcmsSet@rt$corrected[[i]] else
        rtcor <- NULL
        TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
    }

    pdf(pdfname,w=16,h=10)
    cols <- rainbow(N)
    lty = 1:N

    return(as.matrix(md5sum(files)))
}


# This function get the raw file path from the arguments
getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {    
    if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
    if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
    if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]

    if (!is.null(listArguments[["singlefile_galaxyPath"]])) {

27:30410a052ab3

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

#@author G. Le Corguille
exportTicBpcTabular <- function(dataset, filenameBase, ticORbpc, rt='raw') {

        rawORcorrected = ''
        title = ''
        if (rt=='corrected') {
            rawORcorrected = '_corrected'
            title = ' corrected by retcor'
        }

        if (ticORbpc == "TIC") {
            section_name = paste0('TIC',rawORcorrected)
            title = paste0('Total Ion Current (TIC) chromatogram',title)
            description = 'Sum of intensity (Y) of all ions detected at each retention time(X)'
        } else if (ticORbpc == "BPC") {
            section_name = paste0('BPC',rawORcorrected)
            title = paste0('Base Peak Chromatogram (BPC)',title)
            description = 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'
        }

        filename=paste0(basename(file_path_sans_ext(filenameBase)),"-",ticORbpc,rawORcorrected,"_mqc.out")

        # Headers for MultiQC
        cat("# file_format: 'tsv'\n", sep="", file = filename)
        cat("# section_name: '",section_name,"'\n", sep="", file = filename, append = T)
        cat("# title: '",title,"'\n", sep="", file = filename, append = T)
        cat("# description: '",description,"'\n", sep="", file = filename, append = T)
        cat("# plot_type: 'linegraph'\n", sep="", file = filename, append = T)
        cat("# pconfig:\n", sep="", file = filename, append = T)
        cat("#     id: '",ticORbpc,rawORcorrected,"_lineplot'\n", sep="", file = filename, append = T)
        cat("#     ylab: 'Base Peak Intensity'\n", sep="", file = filename, append = T)
        cat("#     xlab: 'Retention Time'\n", sep="", file = filename, append = T)
        cat("Intensity\tRT\n", file = filename, append = T)
        write.table(dataset, filename ,row.names = F, col.names = F, sep = "\t", append = T, quote = F)
}

#@author Y. Guitton
getBPC <- function(file,rtcor=NULL, ...) {
    object <- xcmsRaw(file)
    sel <- profRange(object, ...)
    cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))

            rtcor <- xcmsSet@rt$corrected[[j]]
        else
            rtcor <- NULL

        TIC[[j]] <- getBPC(files[j],rtcor=rtcor)

        exportTicBpcTabular(TIC[[j]], files[j], "BPC", rt=rt)

        # TIC[[j]][,1]<-rtcor
    }

    for (i in 1:N) {
        if (!is.null(xcmsSet) && rt == "corrected")
            rtcor <- xcmsSet@rt$corrected[[i]] else
        rtcor <- NULL
        TIC[[i]] <- getTIC(files[i],rtcor=rtcor)

        exportTicBpcTabular(TIC[[i]], files[i], "TIC", rt=rt)
    }

    pdf(pdfname,w=16,h=10)
    cols <- rainbow(N)
    lty = 1:N

    return(as.matrix(md5sum(files)))
}


# This function get the raw file path from the arguments
getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
    if (!is.null(listArguments[["zipfile"]]))           zipfile = listArguments[["zipfile"]]
    if (!is.null(listArguments[["zipfilePositive"]]))   zipfile = listArguments[["zipfilePositive"]]
    if (!is.null(listArguments[["zipfileNegative"]]))   zipfile = listArguments[["zipfileNegative"]]

    if (!is.null(listArguments[["singlefile_galaxyPath"]])) {