<tool id="acpype_Amber2Gromacs" name="Convert Amber topology and coordinate files to GROMACS format" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>using acpype</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2021.02.05.22.15">acpype</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input1' ./input1.${input1.ext} &&
        ln -s '$input2' ./input2.${input2.ext} &&
        acpype -p './input1.${input1.ext}' -x './input2.${input2.ext}' 
        
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="txt" label="Amber Topology file" help="Topology file (prmtop) generated in Tleap"/>
        <param name="input2" type="data" format="txt" label="Amber Coordinate file" help="Coordinate file (inpcrd) generated in Tleap"/>
    </inputs>
    <outputs>
        <data format="top" name="top_output" label="GROMACS topology file" from_work_dir='*.top'/>
        <data format="gro" name="gro_output" label="GROMACS coordinate file" from_work_dir="*.gro"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="cid1.prmtop"/>
            <param name="input2" value="cid1.inpcrd"/>
            <output name="top_output">
                <assert_contents>
                    <has_line line="[ defaults ]"/>
                    <has_text text="1               2               yes             0.5     0.8333"/>
                    <has_text text=" ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860"/>
                </assert_contents>
            </output>
            <output name="gro_output">
                <assert_contents>
                    <has_text text=" 42"/>
                    <has_text text="    1  UNL   C1    1  41.372  -2.389   7.399"/>
                    <has_text text="    1  UNL  H42   42  41.256  -2.276   7.041"/>
                    <has_text text="   11.59200    12.19000    23.64000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Tool to produce GROMACS topology and coordinate files from systems generated with AmberTools' Tleap.

.. class:: infomark

**Input**

The input files are the standard topology (prmtop) and coordinate (inpcrd) files that are generally produced as outputs when processing a structure through Tleap.

.. class:: infomark

**Outputs**

GROMACS topology (TOP) and coordinate (GRO) files.

    ]]></help>
    <expand macro="citations">
        <citation type="doi">doi:10.1186/1756-0500-5-367</citation>
    </expand>
</tool>