comparison maldi_quant_peakdetection.xml @ 5:e66f552a3c47 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 218c44b9ba1b5f0f47edb743ed70075fb661386e"

4:e9300ef37403

<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.4">
    <description>
        Peak detection, binning and filtering for mass-spectrometry imaging data
    </description>
    <macros>
        <import>maldi_macros.xml</import>

        #elif $infile.ext == 'analyze75'
            cp '${infile.extra_files_path}/hdr' infile.hdr &&
            cp '${infile.extra_files_path}/img' infile.img &&
            cp '${infile.extra_files_path}/t2m' infile.t2m &&
        #else
            ln -s $infile infile.RData &&
        #end if
        Rscript '${maldi_quant_peak_detection}'&&
        mkdir $outfile_imzml.files_path &&
        mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
        mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
        echo "imzML file:" > $outfile_imzml &&
        ls -l "$outfile_imzml.files_path" >> $outfile_imzml

                                              tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
                                              allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
                    ## 2) warp spectra:
                        peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
                }
                peaks_new = peaks_new_list

            #end if

        #end if

        ## QC plot and numbers
        par(mfrow = c(2, 2), oma=c(0,0,2,0))
        for (random_sample in random_spectra){
            plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))}
        title("Aligned spectra", outer=TRUE, line=0)
        minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
        maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
        mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
        medint = round(median(unlist(lapply(peaks,intensity))), digits=2)

5:e66f552a3c47

<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="@VERSION@.5">
    <description>
        Peak detection, binning and filtering for mass-spectrometry imaging data
    </description>
    <macros>
        <import>maldi_macros.xml</import>

        #elif $infile.ext == 'analyze75'
            cp '${infile.extra_files_path}/hdr' infile.hdr &&
            cp '${infile.extra_files_path}/img' infile.img &&
            cp '${infile.extra_files_path}/t2m' infile.t2m &&
        #else
            ln -s '$infile' infile.RData &&
        #end if
        cat '${maldi_quant_peak_detection}' &&
        Rscript '${maldi_quant_peak_detection}' &&
        mkdir $outfile_imzml.files_path &&
        mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
        mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
        echo "imzML file:" > $outfile_imzml &&
        ls -l "$outfile_imzml.files_path" >> $outfile_imzml

                                              tolerance=$method.methods_conditional.tolerance, method="$method.methods_conditional.warping_method",
                                              allowNoMatches=$method.methods_conditional.allow_nomatch, reference = mass_list)
                    ## 2) warp spectra:
                        peaks_new_list = warpMassPeaks(list(peaks[[pixelnb]]), warping_function, emptyNoMatches=$method.methods_conditional.empty_nomatch)
                }
                peaks = peaks_new_list

            #end if

        #end if

        #if $method.methods_conditional.remove_empty:
            print(paste(length(findEmptyMassObjects(peaks)), " empty spectra were removed", sep=" "))

            ## only if there are empty spectra to remove

            if (length(findEmptyMassObjects(peaks))>0)

                {
                    #if $infile.ext == 'rdata'
                        cardinal_coordinates = cardinal_coordinates[-findEmptyMassObjects(peaks),,drop=FALSE] ## remove coordinates of empty spectra for Cardinal RData input
                    #end if

                    peaks = removeEmptyMassObjects(peaks)
            }
        #end if

        ## QC plot and numbers
        par(mfrow = c(2, 2), oma=c(0,0,2,0))

        for (random_sample in random_spectra){


        tryCatch(
                {
                    plot(peaks[[random_sample]], sub="", main=paste0("spectrum ", pixelnames[random_sample]))},
                error=function(cond) {
                    plot(NULL, xlim=c(0,0), ylim=c(0,0), ylab="intensity", xlab="m/z")
                }
            )
}

        title("Aligned spectra", outer=TRUE, line=0)
        minmz = round(min(unlist(lapply(peaks,mass))), digits=4)
        maxmz = round(max(unlist(lapply(peaks,mass))), digits=4)
        mean_features = round(length(unlist(lapply(peaks,mass)))/length(peaks), digits=2)
        medint = round(median(unlist(lapply(peaks,intensity))), digits=2)