annotate overlay_segmentation_mask.xml @ 0:63b2a10b1001 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/overlay_segmentation_mask/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

<tool id="ip_overlay_segmentation" name="Overlay Segmentation Mask" version="0.0.6">
    <description>Overlay Segmentation Mask</description>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="3.0.2">matplotlib</requirement>
        <requirement type="package" version="5.3.0">pillow</requirement>
        <requirement type="package" version="0.10.0">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/overlay_segmentation_mask.py'
        $greyscale 
        #if str($label_option.label) == '--label'
            --label --label_color '$label_option.label_color'
        #end if
        --thickness $thickness
        --stroke_color '$stroke_color'
        '$input_image' '$input_mask' ./tmp.png
       ]]>
    </command>
    <inputs>
        <param name="input_image" type="data" label="Image Source File" format="tif,bmp,jpg,png"/>
        <param name="input_mask" type="data" label="Mask Source File" format="tif,bmp,jpg,png"/>
        <param name="greyscale" type="boolean" checked='true' truevalue='--grey' falsevalue='' label="Image Is Greyscale" />
        <param name="thickness" size="4" type="float" value="0.3" label="Thickness" />
        <param name="stroke_color" type="color" value="#ff0000" label="Stroke Color"/>
        <conditional name="label_option">
            <param name="label" type="boolean" checked='false' truevalue='--label' falsevalue='' label="Plot Labels" />
            <when value=""> </when>
            <when value="--label">
                <param name="label_color" type="color" value="#ffff00" label="Label Color"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="tmp.png" />
    </outputs>
    <tests>
        <test>
            <conditional name="label_option">
                <param name="label" value="--label"/>
                <param name="label_color" value="#ffff00"/>
            </conditional>
            <param name="stroke_color" value="#ffaa00"/>
            <param name="label_option['label']" value="--label"/>
            <param name="input_image" value="sample.tif"/>
            <param name="input_mask" value="sample_seg.tif"/>
            <param name="greyscale" value="--grey"/> 
            <output name="output" value="outt.png" ftype="png" compare="sim_size"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool overlays a segmentation mask over an image.
    </help>
    <citations>
        <citation type="doi">10.7717/peerj.453</citation>
    </citations>
</tool>