Mercurial > repos > chemteam > ambertools_acpype

annotate template_mmpbsa_mmgbsa.j2 @ 10:da6bd1975a71 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7583aecdb001e76ca6ddf440f60de4c534f61c66"
author chemteam
date Mon, 20 Sep 2021 09:48:17 +0000
parents 27ee142314a9
children
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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1 # Template for mmpbsa in Galaxy
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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2 #
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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3 &general
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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4 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }},
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27ee142314a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
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5 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
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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27ee142314a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
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7 {% if calcdetails.gb_pb_calc.calctype == 'gb' %}
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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8 &gb
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27ee142314a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
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9 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 }}
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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27ee142314a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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11 {% elif calcdetails.gb_pb_calc.calctype == 'pb' %}
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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12 &pb
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27ee142314a9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
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13 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 }}
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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15 {% endif %}
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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16 {% if calcdetails.decomposition.decomposition == 'yes' %}
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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17 &decomp
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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18 csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }},
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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20 {% endif %}
c6afbb28f547 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
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