<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.1.0" python_template_version="3.9">
    <description>Perform a tomography reconstruction</description>
    <macros>
        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir center_slice_pngs;
        $__tool_directory__/tomo_reconstruct.py
        -i '$red_stacks'
        -c '$config'
        --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
        --output_data 'output_data.npz'
        --output_config 'output_config.yaml'
        -l '$log'
    ]]></command>
    <inputs>
        <expand macro="common_inputs"/>
        <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
        <section name="center_offsets" title="Reconstruction center axis offsets">
            <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/>
            <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/>
        </section>
    </inputs>
    <outputs>
        <expand macro="common_outputs"/>
        <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
        <collection name="recon_slices" type="list" label="Recontructed slices midway in each dimension">
            <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
        </collection>
    </outputs>
    <help><![CDATA[
        Reconstruct tomography images.
    ]]></help>
    <expand macro="citations"/>
</tool>