annotate antechamber.xml @ 12:4fff93efc0f9 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 27e76b3f6ed12955fd60609aad4043bc9c60cba2"

<tool id="ambertools_antechamber" name="AnteChamber" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
  <description>- Amber's molecular input file processor</description>
  <macros>
    <import>macros.xml</import>
    <token name="@GALAXY_VERSION@">0</token>
  </macros>
  <expand macro="requirements"></expand>
  <command detect_errors="exit_code">
    <![CDATA[
    antechamber -i '$input1'
        -o '$output1'
        -fi '$input1.ext'
        -fo '$selected_output_format'
        -c '$allparams.c'
        -pf '$extraparams.pf'
        #if '$extraparams.usenc'
        -nc '$allparams.nc'
        #end if
        -at '$allparams.at'
        -j '$allparams.j'
        -rn '$allparams.resname'
        -m '$allparams.m'
        ]]>
  </command>
  <inputs>
    <param type="data" name="input1" label="Molecular input (PDB or mol2)" format="pdb,mol2"/>
    <param name="selected_output_format" type="select" label="Select an output file format (mol2 recommended!):">
      <option value="pdb">pdb</option>
      <option value="mol2" selected="true">mol2</option>
    </param>
    <section name="allparams" title="General Parameters" expanded="true">
      <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/>
      <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/>
      <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)">
        <validator type="regex" message="Maximum of 3 characters allowed.">^[a-zA-Z0-9]{1,3}$</validator>
      </param>
      <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)">
        <option value="resp">RESP</option>
        <option selected="True" value="bcc">AM1-BCC</option>
        <option value="cm1">CM1</option>
        <option value="cm2">CM2</option>
        <option value="esp">ESP (Kollman)</option>
        <option value="mul">Mulliken</option>
        <option value="gas">Gasteiger</option>
      </param>
      <param name="at" type="select" label="Atom type" help="Create atom type for the specified forcefield (-at)">
        <option selected="True" value="gaff">gaff</option>
        <option value="gaff2">gaff2</option>
        <option value="amber">amber for PARM94/99/99SB</option>
        <option value="bcc">bcc</option>
        <option value="sybyl">sybyl</option>
      </param>
      <param name="j" type="select" label="Atom type and bond type prediction index" help="Specify how to run predictions (-j)">
        <option value="0">0 - No assignment</option>
        <option value="1">1 - atom type</option>
        <option value="2">2 - full bond types</option>
        <option value="3">3 - part bond types</option>
        <option selected="True" value="4">4 - atom and full bond type (default)</option>
        <option value="5">5 - atom and part bond type</option>
      </param>
    </section>
    <section name="extraparams" title="Additional Parameters" expanded="false">
      <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Remove intermediate files (recommended)" help="(-pf)"/>
      <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Use net charge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/>
    </section>
  </inputs>
  <outputs>
    <data format="mol2" name="output1" label="${tool.name}: structure output">
      <change_format>
        <when input="selected_output_format" value="pdb" format="pdb"/>
        <when input="selected_output_format" value="mol2" format="mol2"/>
        <!-- <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> -->
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input1" value="LigA.mol2"/>
      <section name="allparams">
        <param name="nc" value="-2"/>
        <param name="c" value="AM1-BCC"/>
        <param name="at" value="gaff2"/>
        <param name="j" value="5 - atom and part bond type"/>
      </section>
      <output name="output1" file="LigA_output.mol2" compare="diff" lines_diff="0">
        <assert_contents>
          <has_text text=" 1 C           49.2110    26.9920    85.5530 c2         1 MOL"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="input1" value="LigA.pdb" ftype="pdb"/>
      <param name="selected_output_format" value="pdb"/>
      <section name="allparams">
        <param name="nc" value="-2"/>
        <param name="c" value="AM1-BCC"/>
        <param name="at" value="gaff2"/>
        <param name="j" value="5 - atom and part bond type"/>
      </section>
      <output name="output1" file="LigA_output.pdb" compare="diff" lines_diff="0">
        <assert_contents>
          <has_text text="ATOM      1  C   MOL     1      49.211  26.992  85.553  1.00  0.00           C"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
    <![CDATA[
.. class:: infomark

**What it does**

Antechamber sets up Amber parameters for the input molecules provided.

.. class:: infomark

**How it works**

- Select an input file (mol2, PDB)
- Specify the correct charge, or keep the default charge of 0
- Adjust other parameters as needed.
- Click on Execute

.. class:: infomark

**Outputs created**

- A mol2 or PDB output is created with the forcefield compatible atom names.

.. 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>