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<tool id="spring_model_all" name="SPRING Model-All" version="0.1.0" python_template_version="3.5" license="MIT">
    <description>complex structures</description>
    <requirements>
        <requirement type="package" version="1.78">biopython</requirement>
        <requirement type="package" version="20170708">tmalign</requirement>
        <requirement type="package" version="3.06">pulchra</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python3 '$__tool_directory__/spring_model_all.py' -p '$pairs' -ih '$index_hhr' -dh '$database_hhr' -i '$index_pdb' -d '$database_pdb' -c '$crossreference' -o 'models' -g '$log'
    ]]></command>
    <inputs>
        <param format="tabular" name="pairs" type="data" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs."/>
        <param format="ffindex" name="index_hhr" type="data" label="HHR Index" help="HHR Database Index file (ffindex)."/>
        <param format="ffdata" name="database_hhr" type="data" label="HHR Database" help="HHR Database files (ffdata)."/>
        <param format="ffindex" name="index_pdb" type="data" label="PDB Index" help="PDB Database Index file (ffindex)."/>
        <param format="ffdata" name="database_pdb" type="data" label="PDB Database" help="PDB Database files (ffdata)."/>
        <param format="tabular" name="crossreference" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool."/>
    </inputs>
    <outputs>
        <collection type="list" label="SPRING Model Structures" name="models">
            <discover_datasets pattern="__name_and_ext__" directory="models" />
        </collection>
        <data format="tabular" name="log" label="SPRING Model Log"/>
    </outputs>
    <help><![CDATA[
Creates protein complex model from HHsearch threading results.
    ]]></help>
    <tests>
        <test>
            <param name="pairs" value="model/pairs.txt" />
            <param name="index_hhr" value="model/hhr.ffindex" />
            <param name="database_hhr" value="model/hhr.ffdata" />
            <param name="index_pdb" value="model/pdb_structures.ffindex" />
            <param name="database_pdb" value="model/pdb_structures.ffdata" />
            <param name="crossreference" value="model/crossreference.txt" />
            <output name="log" file="model/log.txt"/>
        </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>