<tool id="spring_model_all" name="SPRING Model-All" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>complex structures</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    spring_model_all.py
        -p '$pairs'
        @hhr_source@
        @pdb_source@
        -c '$crossreference'
        -o 'models'
        -g '$log'
    ]]>    </command>
    <inputs>
        <param name="pairs" type="data" format="tabular" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs." />
        <param name="crossreference" type="data" format="tabular" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
        <expand macro="hhr_source" />
        <expand macro="pdb_source" />
        <expand macro="logfile" />
    </inputs>
    <outputs>
        <collection name="models" type="list" label="SPRING Model Structures">
            <discover_datasets pattern="__name_and_ext__" directory="models" />
        </collection>
        <data format="tabular" name="log" label="SPRING Model Log">
            <filter>logfile</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="pairs" value="model/pairs.txt" ftype="tabular" />
            <conditional name="hhr_source">
                <param name="hhr_source_selector" value="history" />
                <param name="ffindex" value="model/hhr.ffindex" />
                <param name="ffdata" value="model/hhr.ffdata" />
            </conditional>
            <conditional name="pdb_source">
                <param name="pdb_source_selector" value="history" />
                <param name="ffindex" value="model/pdb.ffindex" />
                <param name="ffdata" value="model/pdb.ffdata" />
            </conditional>
            <param name="crossreference" value="model/crossreference.txt" />
            <param name="logfile" value="true" />
            <output name="log" file="model/log.txt" />
            <output_collection name="models" type="list" count="1">
                <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
            </output_collection>
        </test>
        <test>
            <param name="pairs" value="model/pairs.txt" ftype="tabular" />
            <conditional name="hhr_source">
                <param name="hhr_source_selector" value="indexed" />
                <param name="hhr" value="hhr_model" />
            </conditional>
            <conditional name="pdb_source">
                <param name="pdb_source_selector" value="indexed" />
                <param name="pdb" value="pdb01_model" />
            </conditional>
            <param name="crossreference" value="model/crossreference.txt" />
            <param name="logfile" value="true" />
            <output name="log" file="model/log.txt" />
            <output_collection name="models" type="list" count="1">
                <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Creates protein complex model from HHsearch threading results.

    ]]>    </help>
    <expand macro="citations" />
</tool>