annotate extract_top.xml @ 0:9faa4f4b8b76 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b"

<tool id="gromacs_extract_topology" name="Extracting Topology Information" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.09">
    <description>from a GROMACS topology file</description>

    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>

    <expand macro="requirements">
    </expand>

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

            python3 '$__tool_directory__/gmxtras_extract_top.py' --top_file '$inputtopology' --out_nonbondparam '$atomtypes' --out_bondparam '$moltypes'

    ]]></command>
    <inputs>
        <param name="inputtopology" type="data" format="top" label="Topology file we are extracting from" help="We are extracting the information under [ atomtypes ] and [ moleculetype ]."/>
    </inputs>

    <outputs>
        <data name="atomtypes" format="txt" label="Nonbonded parameters and atom types under [ atomtypes ] section ${on_string}">
        </data>
        <data name="moltypes" format="txt" label="Bonded parameters and relevant information under [ moleculetype ] section ${on_string}">
        </data>
    </outputs>
    <tests>
        <test>
            <param name="inputtopology" value="cid1_GMX.top" />
            <output name="atomtypes">
                <assert_contents>
                    <has_text text=" ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860"/>
                    <has_text text=" hn       hn          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ; 0.60  0.0157"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputtopology" value="cid1_GMX.top" />
            <output name="moltypes">
                <assert_contents>
                    <has_text text="     1   ca     1   cid1    C1    1    -0.236300     12.01000 ; qtot -0.236"/>
                    <has_text text="    23      1      4      2      4   180.00   4.60240   2 ;    H23-    C1-    C4-    C2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Tool to extract the [ atomtypes ] and [ moleculetype ] sections from a topology file. Both of these outputs can then be used as inputs in the Add Topologies tool. This tool can be used for a number of purposes, including but not limited to extracting the topology information required to complement the output of "gmx insert-molecules".   

.. class:: infomark

**Input**

The system topology file you are extracting parameters from.

.. class:: infomark

**Outputs**

1) Text file containing the atom types and nonbonded parameters.
2) Text file containing the molecule type information with bonded parameters.


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