annotate parmchk2.xml @ 2:00ff41b1d49a draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

<tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@">
  <description>- Amber's parameter checker</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <command detect_errors="exit_code">
    <![CDATA[
    parmchk2 -i '$input1'
        -f '$input1.ext'
        -s '$allparams.s'
        -a '$allparams.a'
        -o '$output1'
        ]]>
  </command>
  <inputs>
    <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/>
    <section name="allparams" title="General parameters" expanded="true">
      <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)">
        <option selected="True" value="1">1: gaff</option>
        <option value="2">2: gaff2</option>
      </param>
      <param name="a" type="boolean" checked="false" truevalue="Y" falsevalue="N" label="Print all force field parameters" help="(-a)"/>
    </section>
  </inputs>
  <outputs>
    <data format="txt" name="output1" label="${tool.name}: frcmod output"></data>
  </outputs>
  <tests>
    <test>
      <param name="input1" value="LigA_prmchk.mol2"/>
      <section name="allparams">
        <param name="s" value="2"/>
      </section>
      <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output>
    </test>
  </tests>
  <help>
    <![CDATA[
.. class:: infomark

**What it does**

Antechamber parameter check reads in a mol2 file and writes out a force field modification (frcmod) file containing any force field parameters that are needed for the molecule but not supplied by the force field file.
Problematic parameters, if any, are indicated in the frcmod file with the note, “ATTN, need revision”, and are typically given values of zero.


.. class:: infomark

**How it works**

- Select a mol input file (mol2)
- Choose GAFF or GAFF2 parameter set

.. class:: infomark

**Outputs created**

- Outputs a frcmod file as text

.. class:: infomark

**User guide and documentation**

- AmberTools `userguide`_


.. _`userguide`: http://ambermd.org/doc12/Amber19.pdf

.. class:: infomark

**Feature requests**

Go to Galaxy Computational Chemistry and make a `feature request`_

.. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new

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