<tool id="ip_landmark_registration" name="Landmark Registration" version="0.0.2">
    <description>Landmark Registration</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>
    </requirements>
    <command><![CDATA[
         python '$__tool_directory__/landmark_registration.py'
         --residual_threshold $residual_threshold
         --max_trials $max_trials
         '$points_file1'
         '$points_file2'
         '$warp_matrix'
]]></command>
    <inputs>
          <param name="points_file1" type="data" format="tabular" label="Path to tab-separated file with src points" />
          <param name="points_file2" type="data" format="tabular" label="Path to tab-separated file with dst points" />
          <param name="residual_threshold" type="float" value="2" label="Maximum distance for a data point to be classified as an inlier." />
        <param name="max_trials" type="integer" value="100" label="Maximum number of iterations for random sample selection." />
    </inputs>
    <outputs>
       <data format="tabular" name="warp_matrix" />
    </outputs>
    <tests>
        <test>
            <param name="points_file1" value="points1.tsv"/>
            <param name="points_file2" value="points2.tsv"/>
            <param name="residual_threshold" value="2"/>
            <param name="max_trials" value="100"/>
            <output name="warp_matrix" value="warp.tsv" ftype="tabular" compare="diff" lines_diff="6"/>
        </test>
    </tests>
    <help>
    **What it does**

    This tool estimates the transformation matrix between two sets of 2d points.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>