<macros>
    <token name="@VERSION@">0.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.7">python</requirement>
            <requirement type="package" version="0.25.2">yank</requirement>
            <requirement type="package" version="1.6">pdbfixer</requirement>
            <requirement type="package" version="0.6.0">openforcefield</requirement>
            <requirement type="package" version="3.2.0">parmed</requirement>
            <requirement type="package" version="@VERSION@">openduck</requirement>
        </requirements>
    </xml>
    <xml name="interaction_params">
        <section name="ia" title="Parameters for the protein-ligand interaction" expanded="true">
            <param argument="chain_sel" type="text" label="Chain ID for selection" help="E.g. 'A', 'B', etc.">
                <validator type="regex" message="Invalid chain ID">^[A-Z]$</validator>
            </param>
            <param argument="res_sel" type="text" label="Three letter residue code for selection" help="E.g. 'ASP', 'TYR', etc.">
                <validator type="regex" message="Invalid chain ID">^[A-Z]{3}$</validator>
            </param>
            <param argument="resid_sel" type="text" label="Residue ID for selection" help="Position of residue in sequence, e.g. 163">
                <validator type="regex" message="Invalid chain ID">^[0-9]+$</validator>
            </param>
            <param argument="atom_sel" type="text" label="Atom to select within the chosen residue" help="E.g. 'OD2'">
                <validator type="regex" message="Invalid chain ID">^[A-Z0-9]+$</validator>
            </param>
        </section>
    </xml>
    <xml name="tar_param">
        <param argument="return_tar" type="boolean" checked="true" label="Return a tar file?" help="Return a tar file containing all files produced during the simulations."/>
    </xml>
    <xml name="tar_output">
        <data name="tar" format="tar" from_work_dir="allfiles.tar.gz" label="${tool.name} tarball">
            <filter>return_tar</filter>
        </data>
    </xml>
    <xml name="citations">
    <citations>
        <citation type="doi">10.1038/nchem.2660</citation>
        <citation type="bibtex">
@misc{Bradley2019,
  author = {Bradley, Anthony},
  title = {OpenDUck source code},
  year = {2019},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {URL: https://github.com/xchem/duck},
  commit = {b98bb78284e9c92837ac1e69fc2f06306ab1e28c}
}
        </citation>
    </citations>
    </xml>
</macros>