<tool id="gmx_restraints" name="Create GROMACS position restraints files" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using genrestr</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>

    <expand macro="requirements" />

    <command detect_errors="exit_code"><![CDATA[

        ln -s '$gro_input' ./gro_input.gro &&
        ln -s '$ndx_input' ./ndx_input.ndx &&
        echo '$index' | gmx genrestr -f ./gro_input.gro -n ./ndx_input.ndx -o tmp.itp -fc $fc  &>> verbose.txt &&
        tail -n +2 tmp.itp > posre.itp
    ]]></command>

    <inputs>
        <param argument="gro_input" type="data" format='gro' label="GRO input file" help="Input structure"/>
        <param argument="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the atoms which should be restrained"/>
        <param argument="fc" type="text" value="1000 1000 1000" label="Force constants" help="Vector (in Cartesian space) specifying force constants for the restraints (kJ/mol nm^2)">
            <validator type="regex" message="Only numeric values and whitespace allowed">^[0-9 ]*$</validator>
        </param>
        <param argument="index" type="text" label="Index of group" help="Index of group for calculating position restraints - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
            <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
        </param>

        <expand macro="log" />

    </inputs>
    <outputs>
        <data name="output1" format="itp" from_work_dir="posre.itp"/>
        <expand macro="log_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="gro_input" value="str_ions.gro" />
            <param name="ndx_input" value="index.ndx" />
            <param name="fc" value="500 600 700" />
            <param name="index" value="13" />
            <!-- Galaxy seems to think this output is a binary (?) -->
            <output name="output1" file="posre_cl.itp" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool calculates a position restraint (ITP) file for part of a system, specified in provided GRO and NDX files.

_____

.. class:: infomark

**Input**

       - GRO structure file.
       - Index (NDX) file.
       - Force constant vector (in Cartesian space) for applying restraints. E.g. '1000 1000 1000' will apply a force constraint of 1000 kJ/mol nm^2 along each (XYZ) axis.
       - Index number of the group for which restraints should be calculated, i.e. the position of the group in the index file.

_____


.. class:: infomark

**Output**

       - Position restraint (itp) file, which may be useful for system equilibration.

    ]]></help>

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