Repository 'ambertools_antechamber'
hg clone https://toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_antechamber

Changeset 6:e4de81eea04c (2021-01-25)
Previous changeset 5:29aa7091e533 (2020-04-07) Next changeset 7:8029dfe04b28 (2021-02-16)
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
modified:
antechamber.xml
macros.xml
template_mmpbsa_mmgbsa.j2
b
diff -r 29aa7091e533 -r e4de81eea04c antechamber.xml
--- a/antechamber.xml Tue Apr 07 08:01:57 2020 -0400
+++ b/antechamber.xml Mon Jan 25 11:14:14 2021 +0000
b
@@ -1,7 +1,8 @@
-<tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@">
+<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">
b
diff -r 29aa7091e533 -r e4de81eea04c macros.xml
--- a/macros.xml Tue Apr 07 08:01:57 2020 -0400
+++ b/macros.xml Mon Jan 25 11:14:14 2021 +0000
b
@@ -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>
b
diff -r 29aa7091e533 -r e4de81eea04c template_mmpbsa_mmgbsa.j2
--- a/template_mmpbsa_mmgbsa.j2 Tue Apr 07 08:01:57 2020 -0400
+++ b/template_mmpbsa_mmgbsa.j2 Mon Jan 25 11:14:14 2021 +0000
b
@@ -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' %}