comparison mz_images.xml @ 13:a2b57ea6666e draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty"

12:a95a82eb4d50

<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>

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

### only plot images when file has features and pixels: 
par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
if (ncol(msidata)>0 & nrow(msidata) >0){
    if (length(inputmz) != 0){
        for (mass in 1:length(inputmz)){

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))
                title(inputnames[mass], adj = 0.5, line = 1)}


        ## optional svg output with original coordinates
        #if $svg_pixelimage:

            ## works only with MSImageSet as expected
            msidata = as(msidata, "MSImageSet")

            svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
            par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
            print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", normalize.image="$normalize_image"))
            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)
            par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
            print(image(msidata, mz=inputmz, 
                  plusminus = $plusminus_dalton,
                  col=colourvector,
                  contrast.enhance = "$image_contrast", 
                  normalize.image="$normalize_image", 
                  smooth.image = "$image_smoothing",
                  superpose=TRUE, main="overlay of all m/z", 
                  key=FALSE, 
                  ylim= c(maximumy,minimumy)))

             legend("$overlay_cond.legend_position",
                       fill=colourvector,
                      legend=as.numeric(inputmz))

    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <expand macro="reading_2_column_mz_tabular"/>

        <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/>
        <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
            <option value="none" selected="True">none</option>
            <option value="suppression">suppression</option>
            <option value="histogram">histogram</option>
        </param>

            <option value="viridis" selected="True">viridis</option>
            <option value="magma">magma</option>
            <option value="plasma">plasma</option>
            <option value="inferno">inferno</option>
        </param>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of 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">

                <param name="units" value="ppm"/>
            </conditional>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <conditional name="overlay_cond">
                <param name="overlay_selection" value="yes_overlay"/>
                <repeat name="colours">
                    <param name="feature_color" value="#ff00ff"/>
                </repeat>

13:a2b57ea6666e

<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>

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

### only plot images when file has features and pixels: 
par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend

#if str($light_mode) == "white":
    lightmode()
#else
    darkmode()
#end if

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

                print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", 
                smooth.image = "$image_smoothing", colorkey=$colorkey, colorscale=$colorscale, alpha.power=$alpha_power, ylim= c(maximumy,minimumy)))
                title(inputnames[mass], adj = 0.5, line = 1)}


        ## optional svg output with original coordinates
        #if $svg_pixelimage:

            ## works only with MSImageSet as expected
            msidata = as(msidata, "MSImageSet")

            svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy)
            par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
	    #if str($light_mode) == "white":
	        lightmode()
	    #else
	        darkmode()
	    #end if
            print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", alpha.power=$alpha_power, normalize.image="$normalize_image"))
            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)
            print(image(msidata, mz=inputmz, 
                  plusminus = $plusminus_dalton,
                  col=colourvector, 
                  contrast.enhance = "$image_contrast", 
                  normalize.image="$normalize_image", 
                  smooth.image = "$image_smoothing",
                  superpose=TRUE, main="overlay of all m/z", 
                  key=FALSE, alpha.power=$alpha_power,
                  ylim= c(maximumy,minimumy)))

             legend("$overlay_cond.legend_position",
                       fill=colourvector,
                      legend=as.numeric(inputmz))

    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <expand macro="reading_2_column_mz_tabular"/>

        <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/>
        <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots">
            <option value="none" selected="True">none</option>
            <option value="suppression">suppression</option>
            <option value="histogram">histogram</option>
        </param>

            <option value="viridis" selected="True">viridis</option>
            <option value="magma">magma</option>
            <option value="plasma">plasma</option>
            <option value="inferno">inferno</option>
        </param>
        <param name="light_mode" type="select" display="radio" label="Image Background">
            <option value="white" selected="True">white</option>
            <option value="black">black</option>
        </param>
        <param name="alpha_power" type="float" value="1" label="Alpha power" help="Opacity scaling factor (1 is linear)"/>
        <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/>
        <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of 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">

                <param name="units" value="ppm"/>
            </conditional>
            <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/>
            <param name="mz_column" value="1"/>
            <param name="name_column" value="2"/>
            <param name="light_mode" value="black"/>
            <conditional name="overlay_cond">
                <param name="overlay_selection" value="yes_overlay"/>
                <repeat name="colours">
                    <param name="feature_color" value="#ff00ff"/>
                </repeat>