<tool id="tomo_setup" name="Tomo Setup" version="0.1.0" python_template_version="3.9">
    <description>Preprocess tomography images</description>
    <requirements>
        <requirement type="package" version="1.11.0">tomopy</requirement>
        <requirement type="package" version="0.2.12">pyinputplus</requirement>
        <requirement type="package" version="3.6.0">h5py</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cp '$inputfiles' inputfiles.txt &&
        $__tool_directory__/tomo_setup.py
        -i inputfiles.txt
        -c '$config'
        --theta_range '$thetas.theta_start $thetas.theta_end $thetas.num_thetas'
        --dark '$dark'
        --bright '$bright'
        --tomo '$tomo'
        --detectorbounds '$detectorbounds'
        --output_data '$output_data'
        --output_config '$output_config'
        -l '$log'
#for $s in $tomo_sets# ${s.offset} ${s.num} #end for
    ]]></command>
    <configfiles>
         <configfile name="inputfiles"><![CDATA[#slurp
#for $s in $tomo_sets
#for $input in $s.inputs
#echo str($input) + '\t' + $input.element_identifier #
#end for
#end for
]]></configfile>
    </configfiles>
    <inputs>
        <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
        <section name="thetas" title="Tomography angles">
            <param name="theta_start" type="float" min="0.0" max="360.0" value="0.0" label="Lower bound"/>
            <param name="theta_end" type="float" min="0.0" max="360.0" value="0.0" label="Upper bound"/>
            <param name="num_thetas" type="integer" min="0" label="Number of angles"/>
        </section>
        <repeat name='tomo_sets' title="Tomography image sets">
            <param name="inputs" type="data_collection" label="Image file collection"/>
            <param name="offset" type="integer" min="0" label="Image index offset"/>
            <param name="num" type="integer" min="1" label="Number of images"/>
        </repeat>
    </inputs>
    <outputs>
        <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/>
        <data name="dark" format="png" label="Dark field"/>
        <data name="bright" format="png" label="Bright field"/>
        <data name="tomo" format="png" label="First tomography image"/>
        <data name="detectorbounds" format="png" label="Detector bounds"/>
        <data name="output_data" format="npz" label="Preprocessed tomography data"/>
        <data name="output_config" format="txt" label="Output config"/>
        <data name="log" format="txt" label="Log"/>
    </outputs>
    <help><![CDATA[
        Preprocess tomography images.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubsum_files,
  author = {Verberg, Rolf},
  year = {2022},
  title = {Tomo Setup},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {somewhere},
}</citation>
    </citations>

</tool>