view merge_top.xml @ 0:33ed3c26b8c2 draft

planemo upload for repository commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:12:00 -0400
children f2faba46d680
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<tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="0.1.0">
    <description>for example, for protein and ligand files</description>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$top_input' ./ &&
        #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__/' itps.txt
        <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
        <param argument="itp_inputs" type="data" format='itp' multiple="true" label="Position restraint file"/>
        <data name="output" format="top" from_work_dir=""/>
            <param name="top_input" value="" />
            <param name="itp_inputs" value="posres.itp" />
            <output name="output" file="" ftype="top" />
        Use this tool to combine GROMACS topologies - for example, the topology files for a ligand and protein.
    <expand macro="citations" />