<tool id="spring_map" name="SPRING Map" version="0.1.0" python_template_version="3.5" license="MIT">
    <description>with BLAST</description>
    <requirements>
        <requirement type="package" version="2.10.1">blast</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/spring_map.py' -l '$list' -i '$index' -d '$database' -c '$cross' -o '$output' -g '$log' -t temp
    ]]></command>
    <inputs>
        <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`."/>
        <param format="ffindex" name="index" type="data" label="PDB Database Index" help="Database Index file."/>
        <param format="ffdata" name="database" type="data" label="PDB Database" help="Database Data file."/>
        <param format="tabular" name="cross" type="data" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="SPRING Map Cross Reference"/>
        <data format="txt" name="log" label="SPRING Map Log"/>
    </outputs>
    <help><![CDATA[
Creates a 3rd column for the SPRING cross reference containing the chain identifier of the binding partners homologue.
    ]]></help>
    <tests>
        <test>
            <param name="list" value="cross/chains.tabular" />
            <param name="index" value="cross/pdb.ffindex" />
            <param name="database" value="cross/pdb.ffdata" />
            <param name="cross" value="cross/reference.tabular" />
            <output name="output" file="map/mapped.reference.tabular"/>
        </test>
    </tests>
    <citations>
        <citation type="bibtex">
@misc{githubhh-suite,
author = {Guerler, Govindarajoo, Zhang},
year = {2013},
title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
publisher = {ACS Publications},
journal = {Journal of Chemical Information and Modeling},
url = {https://pubs.acs.org/doi/10.1021/ci300579r},
}
        </citation>
    </citations>
</tool>