<tool id="colorize_labels" name="Colorize label map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>with SuperDSM</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">superdsm</xref>
        <xref type="biii">superdsm</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.2.0">superdsm</requirement>
        <requirement type="package" version="1.20">numpy</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
    </requirements>
    <command><![CDATA[
    
    ## Inputs
    
    python '$__tool_directory__/colorize_labels.py' '$input'
    --seed $seed
    --bg_label $bg_label
    --bg_color '$bg_color'
    
    ## Outputs
    
    --output output.png
    
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tiff,png" label="Input image (label map)" />
        <param argument="--seed" type="integer" value="0" label="Randomization seed" />
        <param argument="--bg_label" type="integer" value="0" label="Background label" />
        <param argument="--bg_color" type="color" value="#000000" label="Background color"/>
    </inputs>
    <outputs>
       <data format="png" name="output" from_work_dir="output.png" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input1.tif"/>
            <param name="bg_label" value="0"/>
            <param name="bg_color" value="#5a5a5a"/>
            <output name="output" value="output1.png" ftype="png" compare="sim_size" delta_frac="0.1"/>
        </test>
    </tests>
    <help>
        Colorize a 2-D label map for visualization.

        Label maps are produced by segmentation and other image analysis steps.
        Direct inspection of label maps can be difficult,
        because labels usually correspond to gray values which are difficult to
        distinguish visually from each other and from the image background.
        To facilitate the visual inspection of label maps, this tools converts
        label maps to color images, by assigning each label a unique color.
    </help>
    <citations>
        <citation type="doi">10.1109/TPAMI.2022.3185583</citation>
    </citations>
</tool>