comparison mz_images.xml @ 2:27a4c660bbca draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1

1:4d5f798a7a18

<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.1">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <macros>
        <import>macros.xml</import>

grid.table(property_df, rows= NULL)

############################# II) images ####################################

### only plot images when file has peaks and valid input m/z: 

if (npeaks > 0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

            ###standard image

            #if str($image_type) == "standard_image":
                print("standard image")

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}


            ###lattice image

                #if str($strip) =="TRUE": 

                print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
                lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", 
                colorkey=$colorkey,ylim= c(maximumy+0.1*maximumy,minimumy-0.1*minimumy),
                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}

                #elif str($strip) =="FALSE": 

                print(image(msidata, mz=inputmz[mass], strip = $strip,

            #end if 

        ## optional svg output with original coordinates
        #if $svg_pixelimage:
            print("svg pixel image")
            svg(file="svg_pixel_output.svg")
            par(mar=c(0,0,0,0))
            image(msidata, mz = inputmz[1],strip=FALSE, ylim=c(maximumy, minimumy), plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
            dev.off()
        #end if

    } else {print("The input m/z were invalid")}
    dev.off()
}else{
    print("inputfile has no intensities > 0")
dev.off()
}


    ]]></configfile>

        <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image"
            label="Standard image" help="No: lattice function is used to display image"/>
        <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}"/>
        <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
            <filter>svg_pixelimage</filter>
        </data>
    </outputs>
    <tests>

            <param name="svg_pixelimage" value="True"/>
            <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
            <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
        </test>
        <test>
            <param name="infile" value="preprocessed.rdata" ftype="rdata"/>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="strip" value="True"/>

2:27a4c660bbca

<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2">
    <description>
        mass spectrometry imaging m/z heatmaps
    </description>
    <macros>
        <import>macros.xml</import>

grid.table(property_df, rows= NULL)

############################# II) images ####################################

### only plot images when file has features and pixels: 

if (ncol(msidata)>0 & nrow(msidata) >0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

            ###standard image

            #if str($image_type) == "standard_image":
                print("standard image")

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.2*maximumy,minimumy-1),
                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}


            ###lattice image

                #if str($strip) =="TRUE": 

                print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)),
                lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", 
                colorkey=$colorkey,ylim=c(maximumy+0.2*maximumy,minimumy-1),
                main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))}

                #elif str($strip) =="FALSE": 

                print(image(msidata, mz=inputmz[mass], strip = $strip,

            #end if 

        ## optional svg output with original coordinates
        #if $svg_pixelimage:
            print("svg pixel image")
            ## reverse y axis for svg output = correct order and nice svg image
            coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1
            svg(file="svg_pixel_output.svg")
            par(mar=c(0,0,0,0))
            image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing")
            dev.off()
        #end if

        ## optional overlay all input m/z in one image
        #if str($overlay_cond.overlay_selection) == "yes_overlay":

        #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
        colourvector = c($color_string)

            image(msidata, mz=inputmz, 
                  plusminus = $plusminus_dalton,
                  col=colourvector,
                  contrast.enhance = "$image_contrast", 
                  normalize.image="linear",
                  smooth.image = "$image_smoothing",
                  superpose=TRUE, main="overlay of all m/z", 
                  ylim= c(maximumy+0.2*maximumy,minimumy-1))

                legend("topright",
                       fill=colourvector,
                       legend=as.numeric(sort(as.character(inputmz))))
        #end if

    } else {print("The input m/z were invalid")}
    dev.off()
}else{
    print("input file has no features or pixels left")
dev.off()
}


    ]]></configfile>

        <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image"
            label="Standard image" help="No: lattice function is used to display image"/>
        <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/>
        <conditional name="overlay_cond">
            <param name="overlay_selection" type="select" label="Overlay image">
                <option value="no_overlay" selected="True">no</option>
                <option value="yes_overlay">yes</option>
            </param>
            <when value="no_overlay"/>
            <when value="yes_overlay">
            <repeat name="colours" title="Colours for the plots" min="1" max="50">
                <param name="feature_color" type="color" label="Colours" value="#ff00ff" help="Numbers of colours should be the same as number of m/z in tabular file">
                  <sanitizer>
                    <valid initial="string.letters,string.digits">
                      <add value="#" />
                    </valid>
                  </sanitizer>
                </param>
            </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/>
        <data format="svg" name="svg_output" from_work_dir="svg_pixel_output.svg" label="${tool.name} on ${on_string}: image.svg">
            <filter>svg_pixelimage</filter>
        </data>
    </outputs>
    <tests>

            <param name="svg_pixelimage" value="True"/>
            <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
            <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/>
        </test>
        <test>
            <param name="infile" value="preprocessed.RData" ftype="rdata"/>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="plusminus_dalton" value="0.5"/>
            <param name="strip" value="True"/>