annotate template_mmpbsa_mmgbsa.j2 @ 10:df191be5f11a draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit aa5e1ad9fb06855dddc66b6cdfa2e5724c251c53"
author chemteam
date Wed, 14 Jul 2021 11:28:07 +0000
parents e4de81eea04c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
1 # Template for mmpbsa in Galaxy
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
2 #
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
3 &general
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
4 startframe={{ allparams.startframe }}, endframe={{ allparams.endframe }}, interval={{ allparams.interval }},
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 4
diff changeset
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
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
6 /
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 4
diff changeset
7 {% if calcdetails.gb_pb_calc.calctype == 'gb' %}
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
8 &gb
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 4
diff changeset
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 }}
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
10 /
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 4
diff changeset
11 {% elif calcdetails.gb_pb_calc.calctype == 'pb' %}
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
12 &pb
6
e4de81eea04c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 4a3f58846bcad26240ccdc6b76e8f4d2cbe63631"
chemteam
parents: 4
diff changeset
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 }}
4
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
14 /
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
15 {% endif %}
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
16 {% if calcdetails.decomposition.decomposition == 'yes' %}
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
17 &decomp
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
18 csv_format={{ calcdetails.decomposition.csv_format | int }}, dec_verbose={{ calcdetails.decomposition.dec_verbose }}, idecomp={{ calcdetails.decomposition.idecomp }},
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
19 /
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
20 {% endif %}
ca57ded3ec32 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit a68f9fb01e0cfff122aef8ddce5c866c687a4f9a"
chemteam
parents:
diff changeset
21