diff antechamber.xml @ 0:c01897428864 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/antechamber.xml	Thu Jun 13 03:52:54 2019 -0400
@@ -0,0 +1,148 @@
+<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">
+    <![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)"/>
+      <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 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>
+        <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 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
+
+**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>