<tool id="ip_overlay_images" name="Overlay Images" version="0.0.1" profile="20.05"> 
    <description>for visualization</description>
    <requirements>
        <requirement type="package" version="0.18.1">scikit-image</requirement> 
        <requirement type="package" version="3.3.4">matplotlib</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
        python '$__tool_directory__/overlay_images.py'
        '$im1' '$im2' ./output.tif
        --method '$method_option.method'
        #if '$method_option.method' == 'blending':
            --alpha '$alpha'
        #elif '$method_option.method' == 'seg_contour':
            --thickness '$thickness'
            --color '$color'
            $show_label
        #end if
    ]]>
    </command>
    <inputs>
        <conditional name="method_option">
            <param name="method" type="select" label="How to visualize the overlay?">
                <option value="coloc_vis" selected="True">Colocalization</option>
                <option value="blending">Blending</option>
                <option value="seg_contour">Segmentation mask over image</option>
            </param>
            <when value="coloc_vis">
                <param name="im1" type="data" format="tiff,png" label="Image #1 (red channel)" />
                <param name="im2" type="data" format="tiff,png" label="Image #2 (green channel)" />
            </when>
            <when value="blending">
                <param name="im1" type="data" format="tiff,png" label="Image #1" />
                <param name="im2" type="data" format="tiff,png" label="Image #2" />
                <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: I_out = (1 - w) * I_1 + w * I_2."/>
            </when>
            <when value="seg_contour">
                <param name="im1" type="data" format="tiff,png" label="Image" />
                <param name="im2" type="data" format="tiff,png" label="Label image" />
                <param name="thickness" type="float" value="0.3" label="Contour thickness" />
                <param name="color" type="color" value="#ff0000" label="Contour color"/>
                <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tiff" name="out" from_work_dir="output.tif" />
    </outputs>
    <tests>
        <test>
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <conditional name="method_option">
                <param name="method" value="coloc_vis"/>
            </conditional>
            <output name="out" value="test1.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test>
            <param name="im1" value="mask1.tif"/>
            <param name="im2" value="mask1r.tif"/>
            <conditional name="method_option">
                <param name="method" value="blending"/>
            </conditional>
            <param name="alpha" value="0.3"/>
            <output name="out" value="test2.tif" ftype="tiff" compare="sim_size" delta_frac="0.1"/>
        </test>
        <test>
            <param name="im1" value="sample1.tif"/>
            <param name="im2" value="mask1.tif"/>
            <conditional name="method_option">
                <param name="method" value="seg_contour"/>
            </conditional>
            <param name="thickness" value="0.4"/>
            <param name="color" value="#ffaa00"/>
            <param name="show_label" value="true"/>
            <output name="out" value="test3.tif" ftype="tiff" compare="sim_size" delta="20000" delta_frac="0.2"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool overlays two image to visualize 1) image blending, 2) colocalization, or 3) a segmentation mask over an image.
    </help>
    <citations>
    </citations>
</tool>