Mercurial > repos > chemteam > gmx_em
comparison macros.xml @ 4:c1e98d48b8b4 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:48:06 -0400 |
| parents | 5ced6b7070b6 |
| children | 40835063146c |
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| 3:5ced6b7070b6 | 4:c1e98d48b8b4 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@VERSION@">2019.1</token> | 2 <token name="@VERSION@">2019.1.1</token> |
| 3 <xml name="requirements"> | 3 <xml name="requirements"> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="@VERSION@">gromacs</requirement> | 5 <requirement type="package" version="2019.1">gromacs</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 </xml> | 7 </xml> |
| 8 <xml name="citations"> | 8 <xml name="citations"> |
| 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 <conditional name="mdp"> | 28 <conditional name="mdp"> |
| 15 <param name="mdpfile" type="select" label="Parameter input"> | 29 <param name="mdpfile" type="select" label="Parameter input"> |
| 16 <option value="custom">Upload own MDP file</option> | 30 <option value="custom">Upload own MDP file</option> |
| 17 <option value="default">Use default (partially customisable) setting</option> | 31 <option value="default">Use default (partially customisable) setting</option> |
| 18 </param> | 32 </param> |
| 19 <when value="custom"> | 33 <when value="custom"> |
| 20 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> | 34 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> |
| 21 </when> | 35 </when> |
| 22 <when value="default"> | 36 <when value="default"> |
| 23 <param argument="integrator" type="select" label="Choice of integrator."> | 37 <param argument="integrator" type="select" label="Choice of integrator"> |
| 24 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> | 38 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> |
| 25 <option value="sd">Stochastic dynamics integrator</option> | 39 <option value="sd">Stochastic dynamics integrator</option> |
| 26 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> | 40 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> |
| 27 </param> | 41 </param> |
| 28 <param argument="constraints" type="select" label="Bond constraints (constraints)."> | 42 <param argument="constraints" type="select" label="Bond constraints (constraints)"> |
| 29 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> | 43 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> |
| 30 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> | 44 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> |
| 31 <option value="all-bonds">All bonds (all-bonds).</option> | 45 <option value="all-bonds">All bonds (all-bonds).</option> |
| 32 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> | 46 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> |
| 33 <option value="all-angles">All bonds and angles (all-angles).</option> | 47 <option value="all-angles">All bonds and angles (all-angles).</option> |
| 34 </param> | 48 </param> |
| 35 <param argument="cutoffscheme" type="select" label="Neighbor searching."> | 49 <param argument="cutoffscheme" type="select" label="Neighbor searching"> |
| 36 <option value="Verlet">Generate a pair list with buffering.</option> | 50 <option value="Verlet">Generate a pair list with buffering.</option> |
| 37 <option value="group">Generate a pair list for groups of atoms.</option> | 51 <option value="group">Generate a pair list for groups of atoms.</option> |
| 38 </param> | 52 </param> |
| 39 <param argument="coulombtype" type="select" label="Electrostatics."> | 53 <param argument="coulombtype" type="select" label="Electrostatics"> |
| 40 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> | 54 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> |
| 41 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> | 55 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> |
| 42 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> | 56 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> |
| 43 </param> | 57 </param> |
| 44 | 58 |
| 46 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> | 60 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> |
| 47 <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> | 61 <param argument="write_freq" type="integer" label="Number of steps that elapse between saving data points (velocities, forces, energies)" value="0" min="0" max="1000000" help="Step length in ps." /> |
| 48 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> | 62 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> |
| 49 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> | 63 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/> |
| 50 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> | 64 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> |
| 51 <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" /> | 65 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> |
| 52 | 66 |
| 53 </when> | 67 </when> |
| 54 | 68 |
| 55 </conditional> | 69 </conditional> |
| 56 | |
| 57 <param argument="traj" type="select" label="Trajectory output."> | |
| 58 <option value='none'>Return no trajectory output</option> | |
| 59 <option value='xtc'>Return .xtc file (reduced precision)</option> | |
| 60 <option value='trr'>Return .trr file (full precision)</option> | |
| 61 <option value='both'>Return both .xtc and .trr files</option> | |
| 62 </param> | |
| 63 | 70 |
| 64 <param argument="str" type="select" label="Structure output."> | 71 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> |
| 65 <option value='none'>Return no trajectory output</option> | |
| 66 <option value='gro'>Return .gro file</option> | |
| 67 <option value='pdb'>Return .pdb file</option> | |
| 68 <option value='both'>Return both .gro and .pdb files</option> | |
| 69 </param> | |
| 70 | |
| 71 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
| 72 | 72 |
| 73 | 73 |
| 74 </xml> | 74 </xml> |
| 75 | 75 |
| 76 | 76 |