<tool id="gmx_makendx" name="Create GROMACS index files" version="@VERSION@">
    <description>using make_ndx</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

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

        ln -s '$input_file' ./input.$input_file.ext &&
        (echo '$sel'; echo 'q') | gmx make_ndx -f ./input.$input_file.ext -o ./ndx.ndx &>> verbose.txt &&
        cp ./ndx.ndx '$ndx'

    ]]></command>

    <inputs>
        <param argument="input_file" type="data" format='gro,pdb' label="Input structure"/>
        <param argument="sel" type="text" label="Selection command" help="Selection for the new index group, e.g. 'r34' to select residue 34. Use  the operators '|' (or) and &amp; (and) to combine predefined groups.">
            <sanitizer>
                <valid>
                    <add value="|" />
                    <add value="&amp;" />
                    <add value="!" />
                </valid>
            </sanitizer>
        </param>

        <expand macro="log" />

    </inputs>
    <outputs>
        <data name="ndx" format="ndx"/>
        <expand macro="log_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="md_0_1.gro" ftype="gro"/>
            <param name="sel" value="! 1 &amp; 14" />
            <output name="ndx" file="md_0_1.ndx">
                <assert_contents>
                    <has_line line="[ !Protein_&amp;_non-Water ]"/>
                    <has_text text="38369 38370 38371 38372 38373 38374 38375 38376"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Generates GROMACS custom index files.

_____

.. class:: infomark

**Input**

    - A PDB or GRO file.
    - A selection command for the new index group to be included in the output file. Combine previously defined groups using identifying values with the operators '|' (or) and & (and). For example, '1 | 4' will create a new index group containing all atoms contained within the first and fourth index groups already specified (according to their position in the input file).

_____

.. class:: infomark

**Output**

    - A GROMACS index (ndx) file, containing the 'default' index groups and the new group at the end of the file.

    ]]></help>

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