| Previous changeset 0:6c6cecf51bd0 (2020-04-07) Next changeset 2:b500cc25dd15 (2021-02-16) |
|
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631" |
|
modified:
macros.xml parmconv.xml template_mmpbsa_mmgbsa.j2 |
| b |
| diff -r 6c6cecf51bd0 -r da2252f1ccab macros.xml --- a/macros.xml Tue Apr 07 08:07:39 2020 -0400 +++ b/macros.xml Mon Jan 25 11:15:06 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 6c6cecf51bd0 -r da2252f1ccab parmconv.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[ |
| b |
| diff -r 6c6cecf51bd0 -r da2252f1ccab template_mmpbsa_mmgbsa.j2 --- 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 |
| 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' %} |