| Previous changeset 5:96b872138d3b (2020-04-07) Next changeset 7:79f570a89e3d (2021-02-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631" |
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modified:
macros.xml parmchk2.xml template_mmpbsa_mmgbsa.j2 |
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| diff -r 96b872138d3b -r 6aa2b60f3195 macros.xml --- a/macros.xml Tue Apr 07 07:56:20 2020 -0400 +++ b/macros.xml Mon Jan 25 11:15:31 2021 +0000 |
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| @@ -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> |
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| diff -r 96b872138d3b -r 6aa2b60f3195 parmchk2.xml --- a/parmchk2.xml Tue Apr 07 07:56:20 2020 -0400 +++ b/parmchk2.xml Mon Jan 25 11:15:31 2021 +0000 |
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| @@ -1,7 +1,8 @@ -<tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@"> +<tool id="ambertools_parmchk2" name="ParmChk2" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>- Amber's parameter checker</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements"></expand> <command detect_errors="exit_code"> |
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| diff -r 96b872138d3b -r 6aa2b60f3195 template_mmpbsa_mmgbsa.j2 --- a/template_mmpbsa_mmgbsa.j2 Tue Apr 07 07:56:20 2020 -0400 +++ b/template_mmpbsa_mmgbsa.j2 Mon Jan 25 11:15:31 2021 +0000 |
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| @@ -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' %} |