comparison antechamber.xml @ 2:59a0424937cc draft

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

1:511c4bd8aa6d

<tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@">
  <description>Amber's molecular input file processor</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <command detect_errors="exit_code">

      <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)"/>
      <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 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 netcharge (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>

    <![CDATA[
.. class:: infomark

**What it does**

Antechamber sets up parameters for the input molecules provided.

.. class:: infomark

**How it works**

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

.. class:: infomark

2:59a0424937cc

<tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@">
  <description>- Amber's molecular input file processor</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <command detect_errors="exit_code">

      <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 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>

    <![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