<tool id="ip_image_registration" name="Image Registration" version="0.0.3" profile="20.05"> 
    <description>based on intensity information</description>
    <requirements>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
        <requirement type="package" version="1.6.2">scipy</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
        <requirement type="package" version="2020.10.1">tifffile</requirement>
    </requirements>
    <command detect_errors="aggressive">
    <![CDATA[
         python '$__tool_directory__/image_registration_affine.py'
         '$fn_moving'
         '$fn_fixed'
         '$fn_tmat'
         '$sigma'
         '$metric'
    ]]>
    </command>
    <inputs>
        <param name="fn_moving" type="data" format="tiff,png,jpg" label="Moving image" />
        <param name="fn_fixed" type="data" format="tiff,png,jpg" label="Fixed (reference) image" />
        <param name="sigma" type="float" value="3" label="Sigma of Gaussian filter for smoothing input images" />
        <param name="metric" type="select" label="Image similarity metric">
            <option value="mse" selected="True">Mean squared error</option>
            <option value="mae">Mean absolute error</option>
            <option value="lcc">Local cross-correlation</option>
        </param>
    </inputs>
    <outputs>
       <data format="tabular" name="fn_tmat" />
    </outputs>
    <tests>
      <test>
        <param name="fn_moving" value="moving.png"/>
        <param name="fn_fixed" value="fixed.png"/>
        <param name="sigma" value="3"/>
        <param name="metric" value="lcc"/>
        <output name="fn_tmat" value="tmat.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
      </test>
    </tests>
    <help>
    **What it does**

    This tool estimates the (affine) transformation matrix for registration of two images based on intensity information. 
    </help>
    <citations>
    </citations>
</tool>