annotate overlay_moving_and_fixed_image.xml @ 0:165a9330fc90 draft

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

<tool id="ip_viz_overlay_moving_and_fixed_image" name="Overlay" version="0.0.1">
    <description>moving and fixed image</description>
    <requirements>
        <requirement type="package" version="0.14.2">scikit-image</requirement>
        <requirement type="package" version="0.23.4">pandas</requirement>
        <requirement type="package" version="1.15.4">numpy</requirement>
        <requirement type="package" version="1.1.0">scipy</requirement>
        <requirement type="package" version="5.3.0">pillow</requirement>
    </requirements>
    <command><![CDATA[
         python '$__tool_directory__/overlay_moving_and_fixed_image.py'
             '$fixed_image'
             '$moving_image'
             '$warp_matrix'
             '$overlay_out'
             --factor $factor
             $inverse_transform
    ]]></command>
    <inputs>
        <param name="fixed_image" type= "data" format="png" label="Fixed image" />
        <param name="moving_image" type= "data" format="png" label="Moving image" />
        <param name="warp_matrix" type= "data" format="tabular" label="Warp Matrix" />
        <param name="factor" type="float" value="0.5"
            label="Factor by which images are blended. 1.0 returns a copy of the fixed image, 0.0 returns a copy of the moving image."/>
        <param name="inverse_transform" type="boolean" checked="false" truevalue="--inverse_transform" falsevalue=""
            label="Set to Yes if inverse transformation should be displayed" />
    </inputs>
    <outputs>
       <data format="png" name="overlay_out" />
    </outputs>
    <tests>
      <test>
        <param name="fixed_image" value="sample1.png" />
        <param name="moving_image" value="sample2.png" />
        <param name="warp_matrix" value="warp_matrix.tsv" />
        <param name="factor" value="0.75" />
        <output name="overlay_out" value="out.png" ftype="png" compare="sim_size" />
      </test>
    </tests>
    <help>
    **What it does**

    This tool performs an overlay of two images of which one was transformed to match the other.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>