Mercurial > repos > chemteam > ambertools_acpype
changeset 5:27ee142314a9 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
| author | chemteam |
|---|---|
| date | Mon, 25 Jan 2021 11:15:57 +0000 |
| parents | f4230f116196 |
| children | 2417677038b2 |
| files | acpype.xml macros.xml template_mmpbsa_mmgbsa.j2 |
| diffstat | 3 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/acpype.xml Tue Apr 07 08:10:40 2020 -0400 +++ b/acpype.xml Mon Jan 25 11:15:57 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@VERSION@"> +<tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>using acpype</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements"> - <requirement type="package" version="2019.10.05.12.26">acpype</requirement> + <requirement type="package" version="2020.10.24.12.16">acpype</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ ln -s '$input1' ./input1.${input1.ext} &&
--- a/macros.xml Tue Apr 07 08:10:40 2020 -0400 +++ b/macros.xml Mon Jan 25 11:15:57 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/template_mmpbsa_mmgbsa.j2 Tue Apr 07 08:10:40 2020 -0400 +++ b/template_mmpbsa_mmgbsa.j2 Mon Jan 25 11:15:57 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' %}