<tool id="spring_cross" name="SPRING Cross" version="0.1.0" python_template_version="3.5" license="MIT">
    <description>reference builder</description>
    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/spring_cross.py' -l '$list' -i '$index' -d '$database' -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="tabular" name="index" type="data" label="PDB Database Index" help="Database Index file (ffindex)."/>
        <param format="data" name="database" type="data" label="PDB Database" help="Database Data file (ffdata)."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="SPRING Cross Reference"/>
        <data format="txt" name="log" label="SPRING Cross Log"/>
    </outputs>
    <help><![CDATA[
Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database. This reference is required as 
input for the SPRING min-Z calculator.
    ]]></help>
    <tests>
        <test>
            <param name="list" value="cross/chains.tabular" />
            <param name="index" value="cross/pdb.ffindex" />
            <param name="database" value="cross/pdb.ffdata" />
            <output name="output" file="cross/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>