<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.1.0" python_template_version="3.9">
    <description>Perform a tomography reconstruction</description>
    <requirements>
        <requirement type="package" version="1.11.0">tomopy</requirement>
        <requirement type="package" version="3.6.0">h5py</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        $__tool_directory__/tomo_reconstruct.py
        -i '$red_stacks'
        -c '$config'
        --output_data 'output.npz'
        --output_config 'output_config.yaml'
        -l '$log'
    ]]></command>
    <inputs>
        <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
        <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
    </inputs>
    <outputs>
        <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
        <data name="output_config" format="yaml" label="Output config" from_work_dir="output_config.yaml"/>
        <data name="log" format="txt" label="Log"/>
    </outputs>
    <help><![CDATA[
        Reconstruct tomography images.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubsum_files,
  author = {Verberg, Rolf},
  year = {2022},
  title = {Tomo Reconstruction},
}</citation>
    </citations>

</tool>