Mercurial > repos > chemteam > ambertools_acpype

diff acpype.xml @ 6:2417677038b2 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c440a43396b4d815ef35f45ed562e22bf37c028"
author chemteam
date Tue, 16 Feb 2021 21:55:56 +0000
parents 27ee142314a9
children 710301bc46fa
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line diff
--- a/acpype.xml	Mon Jan 25 11:15:57 2021 +0000
+++ b/acpype.xml	Tue Feb 16 21:55:56 2021 +0000
@@ -2,7 +2,7 @@
     <description>using acpype</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="2020.10.24.12.16">acpype</requirement>
@@ -14,6 +14,7 @@
             -b base
             -m '$multiplicity'
             -a '$atomtype'
+            -c '$charge_method'
             -o gmx
     ]]></command>
     <inputs>
@@ -26,6 +27,11 @@
             <option value="gaff2">gaff2</option>
             <option value="amber2">AMBER14SB + gaff2</option>
         </param>
+        <param name="charge_method" type="select" value="bcc" label="Charge method">
+            <option value="bcc">bcc (default)</option>
+            <option value="gas">gas</option>
+            <option value="user">charges provided by user in mol2 file</option>
+        </param>
         <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/>
     </inputs>
     <outputs>
@@ -38,6 +44,7 @@
         <test>
             <param name="input1" value="JZ4.mol2"/>
             <param name="save_gro" value="True"/>
+            <param name="charge_method" value="bcc"/>
             <output name="output">
                 <assert_contents>
                     <has_line line="[ atoms ]"/>
@@ -47,6 +54,12 @@
             </output>
             <output name="gro_output" file="base_GMX.gro" lines_diff="2"/>
         </test>
+        <test>
+            <param name="input1" value="LigA_output.mol2"/>
+            <param name="save_gro" value="false"/>
+            <param name="charge_method" value="user"/>
+            <output name="output" file="LigA_output.top" lines_diff="26"/>
+        </test>
     </tests>
     <help><![CDATA[
 Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools.