annotate anisotropic_diffusion.xml @ 2:e6987afa0484 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/anisotropic-diffusion/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

<tool id="ip_anisotropic_diffusion" name="Apply anisotropic diffusion" version="0.2-2"> 
    <description>with MedPy</description>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="0.3.0">medpy</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="0.15.1">tifffile</requirement>
    </requirements> 
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/anisotropic_diffusion.py' '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption'
        ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="tiff" label="Image file"/>
        <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
        <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
        <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
        <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation">
            <option value="1" selected="True">Favour high contrast edges</option>
            <option value="2">Favour wide regions</option>
        </param>
    </inputs>
    <outputs>
        <data format="tiff" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="galaxyIcon_noText.tif" />
            <param name="niter" value="100" />
            <param name="kappa" value="50" />
            <param name="gamma" value="0.1" />
            <param name="eqoption" value="1" />
            <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
        </test>
    </tests>
    <help>
    **What it does**

    Edge-preserving, Anisotropic image diffusion
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>