view parmchk2.xml @ 5:96b872138d3b draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
author chemteam
date Tue, 07 Apr 2020 07:56:20 -0400
parents 00ff41b1d49a
children 6aa2b60f3195
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<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>