Mercurial > repos > chemteam > gmx_em
changeset 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 |
| files | macros.xml minim.xml |
| diffstat | 2 files changed, 52 insertions(+), 26 deletions(-) [+] |
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--- a/macros.xml Fri Aug 30 15:04:13 2019 -0400 +++ b/macros.xml Mon Oct 07 12:48:06 2019 -0400 @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">2019.1</token> + <token name="@VERSION@">2019.1.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">gromacs</requirement> + <requirement type="package" version="2019.1">gromacs</requirement> </requirements> </xml> <xml name="citations"> @@ -11,32 +11,46 @@ </citations> </xml> <xml name="md_inputs"> + <param argument="traj" type="select" label="Trajectory output"> + <option value='none'>Return no trajectory output</option> + <option value='xtc'>Return .xtc file (reduced precision)</option> + <option value='trr'>Return .trr file (full precision)</option> + <option value='both'>Return both .xtc and .trr files</option> + </param> + + <param argument="str" type="select" label="Structure output"> + <option value='none'>Return no structure output</option> + <option value='gro'>Return .gro file</option> + <option value='pdb'>Return .pdb file</option> + <option value='both'>Return both .gro and .pdb files</option> + </param> + <conditional name="mdp"> <param name="mdpfile" type="select" label="Parameter input"> <option value="custom">Upload own MDP file</option> <option value="default">Use default (partially customisable) setting</option> </param> <when value="custom"> - <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> + <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/> </when> <when value="default"> - <param argument="integrator" type="select" label="Choice of integrator."> + <param argument="integrator" type="select" label="Choice of integrator"> <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> <option value="sd">Stochastic dynamics integrator</option> <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> </param> - <param argument="constraints" type="select" label="Bond constraints (constraints)."> + <param argument="constraints" type="select" label="Bond constraints (constraints)"> <option value="none">No constraints except for those defined explicitly in the topology (none).</option> <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> <option value="all-bonds">All bonds (all-bonds).</option> <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> <option value="all-angles">All bonds and angles (all-angles).</option> </param> - <param argument="cutoffscheme" type="select" label="Neighbor searching."> + <param argument="cutoffscheme" type="select" label="Neighbor searching"> <option value="Verlet">Generate a pair list with buffering.</option> <option value="group">Generate a pair list for groups of atoms.</option> </param> - <param argument="coulombtype" type="select" label="Electrostatics."> + <param argument="coulombtype" type="select" label="Electrostatics"> <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> <option value="Reaction-Field-zero">Reaction field electrostatics.</option> @@ -48,27 +62,13 @@ <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> <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."/> <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> - <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" /> + <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> </when> </conditional> - - <param argument="traj" type="select" label="Trajectory output."> - <option value='none'>Return no trajectory output</option> - <option value='xtc'>Return .xtc file (reduced precision)</option> - <option value='trr'>Return .trr file (full precision)</option> - <option value='both'>Return both .xtc and .trr files</option> - </param> - <param argument="str" type="select" label="Structure output."> - <option value='none'>Return no trajectory output</option> - <option value='gro'>Return .gro file</option> - <option value='pdb'>Return .pdb file</option> - <option value='both'>Return both .gro and .pdb files</option> - </param> - - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </xml>
--- a/minim.xml Fri Aug 30 15:04:13 2019 -0400 +++ b/minim.xml Mon Oct 07 12:48:06 2019 -0400 @@ -47,8 +47,6 @@ <inputs> <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> - <conditional name="mdp"> <param name="mdpfile" type="select" label="Parameter input"> <option value="custom">Upload own MDP file</option> @@ -81,6 +79,7 @@ <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> </when> </conditional> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </inputs> <outputs> <data name="output1" format="gro" from_work_dir="em.gro"/> @@ -115,7 +114,34 @@ </tests> <help><![CDATA[ -Upload GRO and TOP files for energy minimisation. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options. +.. class:: infomark + +**What it does** + +This tool performs energy minimization of a system prior to a GROMACS simulation. + +_____ + +.. class:: infomark + +**Input** + + - GRO structure file. + - Topology (TOP) file. + - MDP parameter file (optional) + +To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options. + +.. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html + +_____ + + +.. class:: infomark + +**Output** + + - GRO structure file. ]]></help>