comparison msi_qualitycontrol.xml @ 3:f6aa0cff777c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa

2:1ccbda92b76b

<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.1">
    <description>
        mass spectrometry imaging QC
    </description>
    <requirements>
        <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>

               "Normalization", 
               "Smoothing",
               "Baseline reduction",
               "Peak picking",
               "Centroided", 
               "# valid input masses")

values = c(paste0(maxfeatures), 
           paste0(minmz, " - ", maxmz), 
           paste0(pixelcount), 
           paste0(minimumx, " - ", maximumx),  

           paste0(normalizationinfo),
           paste0(smoothinginfo),
           paste0(baselinereductioninfo),
           paste0(peakpickinginfo),
           paste0(centroidedinfo), 
           paste0(length(inputmasses)))


property_df = data.frame(properties, values)

######################################## PDF #############################################

        #for $foldchanges in $calibrantratio:
            mass1 = $foldchanges.mass1
            mass2 = $foldchanges.mass2
            distance = $foldchanges.distance

            ### find rows which contain masses: 

            mzrowdown1 = features(msidata, mz = mass1-distance)
            mzrowup1 = features(msidata, mz = mass1+distance)
            mzrowdown2 = features(msidata, mz = mass2-distance)

            foldchange = log2(mass1vector/mass2vector)

            ratiomatrix = cbind(foldchange, coord(msidata))

            print(ggplot(ratiomatrix, aes(x=x, y=y, fill=foldchange), colour=colo)
             +scale_y_reverse() + geom_tile() + coord_fixed()
             + ggtitle(paste0("Fold change ", mass1, " Da / ", mass2, " Da"))
             + theme_bw()
             + theme(text=element_text(family="ArialMT", face="bold", size=12))
             + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
                                    ,space = "Lab", na.value = "black", name ="FC"))
        #end for
    #end if

    ## 3) Calibrant images:

    if (length(inputmasses) != 0)
    {   for (mass in 1:length(inputmasses))
        {
          image(msidata, mz=inputmasses[mass], plusminus=$plusminusinDalton, 
                main= paste0("3",LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2), " Da)"), 
                contrast.enhance = "histogram", ylim=c(maxy+1, 0))
        }
    } else {print("3) The inputpeptide masses were outside the mass range")}

    ## 4) Number of peaks per pixel - image

}

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infile" type="data" format="imzml, rdata, analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
            help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
        <param name="filename" type="text" value="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
        <param name="inputpeptidefile" type="data" optional="true" format="txt, csv" label="Text file with peptidemasses and names"
            help="first column peptide m/z, second column peptide name, tab separated file"/>
        <param name="inputcalibrants" type="data" optional="true" format="txt,csv"

        <param name="plusminusinDalton" value="0.25" type="text" label="Mass range" help="plusminus mass window in Dalton"/>
        <repeat name="calibrantratio" title="Plot fold change of two masses for each spectrum" min="0" max="10">
            <param name="mass1" value="1111" type="float" label="Mass 1" help="First mass in Dalton"/>
            <param name="mass2" value="2222" type="float" label="Mass 2" help="Second mass in Dalton"/>
            <param name="distance" value="0.25" type="float" label="Distance in Dalton" help="Distance in Da used to find peak maximum from input masses in both directions"/>
        </repeat>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on $infile.display_name"/>
    </outputs>

3:f6aa0cff777c

<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.2">
    <description>
        mass spectrometry imaging QC
    </description>
    <requirements>
        <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>

               "Normalization", 
               "Smoothing",
               "Baseline reduction",
               "Peak picking",
               "Centroided", 
                paste0("# valid masses in ", "$filename"))

values = c(paste0(maxfeatures), 
           paste0(minmz, " - ", maxmz), 
           paste0(pixelcount), 
           paste0(minimumx, " - ", maximumx),  

           paste0(normalizationinfo),
           paste0(smoothinginfo),
           paste0(baselinereductioninfo),
           paste0(peakpickinginfo),
           paste0(centroidedinfo), 
           paste0(length(inputmasses), "/", length(calibrant_list[,1])+length(input_list[,1])))


property_df = data.frame(properties, values)

######################################## PDF #############################################

        #for $foldchanges in $calibrantratio:
            mass1 = $foldchanges.mass1
            mass2 = $foldchanges.mass2
            distance = $foldchanges.distance

            #if not str($foldchanges.filenameratioplot).strip():
                #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
            #else:
                #set $label = $foldchanges.filenameratioplot
            #end if

            ### find rows which contain masses: 

            mzrowdown1 = features(msidata, mz = mass1-distance)
            mzrowup1 = features(msidata, mz = mass1+distance)
            mzrowdown2 = features(msidata, mz = mass2-distance)

            foldchange = log2(mass1vector/mass2vector)

            ratiomatrix = cbind(foldchange, coord(msidata))

            print(ggplot(ratiomatrix, aes(x=x, y=y, fill=foldchange), colour=colo)
             + geom_tile() + coord_fixed()
             + ggtitle("$label")
             + theme_bw()
             + theme(text=element_text(family="ArialMT", face="bold", size=12))
             + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
                                    ,space = "Lab", na.value = "black", name ="FC"))
        #end for
    #end if

    ## 3) Calibrant images:

    par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
    if (length(inputmasses) != 0)
    {   for (mass in 1:length(inputmasses))
        {
          image(msidata, mz=inputmasses[mass], plusminus=$plusminusinDalton, 
          main= paste0("3", LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminusinDalton, " Da)"),
                contrast.enhance = "histogram", ylim=c(maxy+1, 0))
        }
    } else {print("3) The inputpeptide masses were outside the mass range")}

    ## 4) Number of peaks per pixel - image

}

    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
            help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
        <param name="filename" type="text" value="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
        <param name="inputpeptidefile" type="data" optional="true" format="txt, csv" label="Text file with peptidemasses and names"
            help="first column peptide m/z, second column peptide name, tab separated file"/>
        <param name="inputcalibrants" type="data" optional="true" format="txt,csv"

        <param name="plusminusinDalton" value="0.25" type="text" label="Mass range" help="plusminus mass window in Dalton"/>
        <repeat name="calibrantratio" title="Plot fold change of two masses for each spectrum" min="0" max="10">
            <param name="mass1" value="1111" type="float" label="Mass 1" help="First mass in Dalton"/>
            <param name="mass2" value="2222" type="float" label="Mass 2" help="Second mass in Dalton"/>
            <param name="distance" value="0.25" type="float" label="Distance in Dalton" help="Distance in Da used to find peak maximum from input masses in both directions"/>
            <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/>
        </repeat>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on $infile.display_name"/>
    </outputs>