view merge_top.xml @ 0:2f5e955d7ea5 draft

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<tool id="gmx_merge_files_daimoners" name="Merge GROMACS topologies daimoners version" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>and GRO files</description>
    <macros>
        <token name="@TOOL_VERSION@">3.2.0</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">parmed</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        cat $main_top $mol_top $itp_file > complete.top
    ]]></command>
    <inputs>
        <param name="main_top" type="data" format='top' label="Main topology (TOP) file" help="Main topology file."/>
        <param name="mol_top" type="data" format='top,itp' label="Molecule topology (TOP or ITP) file" help="Molecule topology file. Either TOP or ITP format."/>
        <param name="itp_file" type="data" format='itp' label="Force field (ITP) file" help="Force field ITP file."/>
    </inputs>
    <outputs>
        <data name="complete_top" format="top" from_work_dir="complete.top"/>
    </outputs>
    <tests>
        <test>
            <param name="prot_top" value="topol.top" />
            <param name="lig_top" value="lig.itp" />
            <param name="prot_gro" value="newbox.gro" />
            <param name="lig_gro" value="lig.gro" />
            <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/>
            <output name="complex_gro" file="complex.gro" ftype="gro"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool merges topology and force-field GROMACS files.

_____

.. class:: infomark

**Input**

       - TOP file for the description of the system.
       - A TOP or ITP file for the molecular topology.
       - A ITP force-field file.
_____

        
.. class:: infomark

**Output**

       - TOP overall file.

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{parmed_2020,
author = {Jason Swails and other contributors},
title = {ParmEd},
url={https://github.com/ParmEd/ParmEd},
abstract = {Parameter/topology editor and molecular simulator.},
urldate = {2020-04-03},
publisher = {GitHub},
year = {2020},
month = mar, }</citation>
    </citations>
</tool>