<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" 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;
            $__tool_directory__/tomo_reconstruct.py
            --input_file '$input_file'
            --center_file '$center_file'
            --output_file 'output.nex'
            --galaxy_flag
            #if str($center_offsets.type_selector) == "offsets_manual"
                --center_offsets $center_offsets.low $center_offsets.upp
            #end if
            -l '$log'
        ]]>
    </command>
    <inputs>
        <expand macro="common_inputs"/>
        <param name="input_file" type='data' format='nex' optional='false' label="Reduced tomography data"/>
        <param name="center_file" type='data' format='yaml' optional='false' label="Center axis input file"/>
        <conditional name="center_offsets">
            <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually">
                <option value="offsets_from_file" selected="true">Read center axis offsets from file</option>
                <option value="offsets_manual">Manually enter center axis offsets</option>
            </param>
            <when value="offsets_from_file"/>
            <when value="offsets_manual">
                <param name="low" type="float" value = "0" optional="false" label="Lower center offset"/>
                <param name="upp" type="float" value = "0" optional="false" label="Upper center offset"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="common_outputs"/>
        <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension">
            <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
        </collection>
        <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
    </outputs>
    <help><![CDATA[
        Reconstruct tomography images.
    ]]></help>
    <expand macro="citations"/>
</tool>