Mercurial > repos > chemteam > parmconv

changeset 1:da2252f1ccab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
author chemteam
date Mon, 25 Jan 2021 11:15:06 +0000
parents 6c6cecf51bd0
children b500cc25dd15
files macros.xml parmconv.xml template_mmpbsa_mmgbsa.j2
diffstat 3 files changed, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Apr 07 08:07:39 2020 -0400
+++ b/macros.xml	Mon Jan 25 11:15:06 2021 +0000
@@ -1,8 +1,8 @@
 <macros>
-  <token name="@VERSION@">19.11</token>
+  <token name="@TOOL_VERSION@">20.15</token>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="19.11">ambertools</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">ambertools</requirement>
       <yield/>
     </requirements>
   </xml>
--- a/parmconv.xml	Tue Apr 07 08:07:39 2020 -0400
+++ b/parmconv.xml	Mon Jan 25 11:15:06 2021 +0000
@@ -1,12 +1,13 @@
-<tool id="parmconv" name="Convert Parameters" version="@VERSION@">
+<tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
   <description>to AMBER prmtop in preparation for MMPBSA</description>
   <macros>
     <import>macros.xml</import>
+    <token name="@GALAXY_VERSION@">0</token>
   </macros>
   <expand macro="requirements">
     <requirement type="package" version="3.2.0">parmed</requirement>
-    <requirement type="package" version="2019.1">gromacs</requirement>
-    <requirement type="package" version="2.11.1">jinja2</requirement>
+    <requirement type="package" version="2020.4">gromacs</requirement>
+    <requirement type="package" version="2.11.2">jinja2</requirement>
   </expand>
   <command detect_errors="exit_code">
     <![CDATA[
--- a/template_mmpbsa_mmgbsa.j2	Tue Apr 07 08:07:39 2020 -0400
+++ b/template_mmpbsa_mmgbsa.j2	Mon Jan 25 11:15:06 2021 +0000
@@ -2,16 +2,15 @@
 #  
 &general
 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }},
-verbose={{ allparams.verbose }}, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}
+verbose=2, keep_files={{ allparams.keep_files | int }}, strip_mask={{ allparams.strip_mask }}, use_sander={{ allparams.use_sander | int }}, entropy={{ allparams.entropy | int }}, netcdf=1
 /
-{% if calcdetails.gbcalc.calctype == 'yes' %}
+{% if calcdetails.gb_pb_calc.calctype == 'gb' %}
 &gb
-igb={{ calcdetails.gbcalc.igb }}, saltcon={{ calcdetails.gbcalc.saltcon }}
+igb={{ calcdetails.gb_pb_calc.igb }}, saltcon={{ calcdetails.gb_pb_calc.saltcon }}, surfoff={{ calcdetails.gb_pb_calc.surfoff }}, molsurf={{ calcdetails.gb_pb_calc.molsurf | int}}, probe={{ calcdetails.gb_pb_calc.probe }}, msoffset={{ calcdetails.gb_pb_calc.msoffset }}
 /
-{% endif %}
-{% if calcdetails.pbcalc.calctype == 'yes' %}
+{% elif calcdetails.gb_pb_calc.calctype == 'pb' %}
 &pb
-istrng={{ calcdetails.pbcalc.istrng }}, fillratio={{ calcdetails.pbcalc.fillratio }}, inp={{ calcdetails.pbcalc.inp }},radiopt={{ calcdetails.pbcalc.radiopt }}
+istrng={{ calcdetails.gb_pb_calc.istrng }}, fillratio={{ calcdetails.gb_pb_calc.fillratio }}, inp={{ calcdetails.gb_pb_calc.inp }}, radiopt={{ calcdetails.gb_pb_calc.radiopt }}, cavity_offset={{ calcdetails.gb_pb_calc.cavity_offset }}, scale={{ calcdetails.gb_pb_calc.scale }}, linit={{ calcdetails.gb_pb_calc.linit }}, prbrad={{ calcdetails.gb_pb_calc.prbrad }}
 /
 {% endif %}
 {% if calcdetails.decomposition.decomposition == 'yes' %}