<tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@VERSION@">
    <description>for example, for protein and ligand files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$top_input' ./top_input.top &&
        #for $itp_input in $itp_inputs
            ln -s '$itp_input' ./$itp_input.element_identifier &&
            echo '$itp_input.element_identifier' >> ./itps.txt &&
        #end for

        python '$__tool_directory__/merge_top.py' top_input.top itps.txt
    ]]></command>
    <inputs>
        <param name="top_input" type="data" format='top' label="Topology (TOP) file" help="'Master' topology into which subordinate topologies will be added."/>
        <param name="itp_inputs" type="data" format='top,itp' multiple="true" label="Topologies (TOP or ITP)" help="One or more topologies for insertion into the main topology. Either TOP or ITP format. Can include position restraint files."/>
    </inputs>
    <outputs>
        <data name="output" format="top" from_work_dir="top_output.top"/>
    </outputs>
    <tests>
        <test>
            <param name="top_input" value="topol.top" />
            <param name="itp_inputs" value="posres.itp" />
            <output name="output" file="top_output.top" ftype="top" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool merges GROMACS topologies - for example, the topology files for a ligand and protein. TOP files contain references to other subordinate TOP files using the `#include` tag. In Galaxy, these tags need to be replaced directly with the contents of the topology files they refer to.

_____

.. class:: infomark

**Input**

       - TOP file for the main topology
       - One or more subordinate topologies (TOP or ITP) which can be inserted into the main topology if specified by an `#include` tag.

_____

        
.. class:: infomark

**Output**

       - TOP file.

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