Mercurial > repos > chemteam > gmx_sim
comparison macros.xml @ 2:5642f48f5698 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
| author | chemteam |
|---|---|
| date | Wed, 20 Nov 2019 11:13:22 -0500 |
| parents | ec3f665cca3e |
| children | 4dba9a5b74fc |
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| 1:ec3f665cca3e | 2:5642f48f5698 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@VERSION@">2019.1.2</token> | 2 <token name="@VERSION@">2019.1.3</token> |
| 3 <xml name="requirements"> | 3 <xml name="requirements"> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="2019.1">gromacs</requirement> | 5 <requirement type="package" version="2019.1">gromacs</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 </xml> | 7 </xml> |
| 9 <citations> | 9 <citations> |
| 10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> | 10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> |
| 11 </citations> | 11 </citations> |
| 12 </xml> | 12 </xml> |
| 13 <xml name="md_inputs"> | 13 <xml name="md_inputs"> |
| 14 <param argument="traj" type="select" label="Trajectory output"> | |
| 15 <option value='none'>Return no trajectory output</option> | |
| 16 <option value='xtc'>Return .xtc file (reduced precision)</option> | |
| 17 <option value='trr'>Return .trr file (full precision)</option> | |
| 18 <option value='both'>Return both .xtc and .trr files</option> | |
| 19 </param> | |
| 20 | |
| 21 <param argument="str" type="select" label="Structure output"> | |
| 22 <option value='none'>Return no structure output</option> | |
| 23 <option value='gro'>Return .gro file</option> | |
| 24 <option value='pdb'>Return .pdb file</option> | |
| 25 <option value='both'>Return both .gro and .pdb files</option> | |
| 26 </param> | |
| 27 | 14 |
| 28 <conditional name="mdp"> | 15 <conditional name="mdp"> |
| 29 <param name="mdpfile" type="select" label="Parameter input"> | 16 <param name="mdpfile" type="select" label="Parameter input"> |
| 30 <option value="custom">Upload own MDP file</option> | 17 <option value="custom">Upload own MDP file</option> |
| 31 <option value="default">Use default (partially customisable) setting</option> | 18 <option value="default">Use default (partially customisable) setting</option> |
| 71 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> | 58 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> |
| 72 | 59 |
| 73 | 60 |
| 74 </xml> | 61 </xml> |
| 75 | 62 |
| 63 <xml name="log"> | |
| 64 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
| 65 </xml> | |
| 66 | |
| 67 <xml name="log_outputs"> | |
| 68 <data name="report" format="txt" from_work_dir="verbose.txt"> | |
| 69 <filter>capture_log</filter> | |
| 70 </data> | |
| 71 </xml> | |
| 76 | 72 |
| 77 <xml name="test_params"> | 73 <xml name="test_params"> |
| 78 <param name="mdpfile" value="default" /> | 74 <param name="mdpfile" value="default" /> |
| 79 <param name="step_length" value="0.002"/> | 75 <param name="step_length" value="0.002"/> |
| 80 <param name="md_steps" value="500"/> | 76 <param name="md_steps" value="500"/> |