Mercurial > repos > chemteam > gmx_energy
view macros.xml @ 14:593c63b5aff8 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"
author | chemteam |
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date | Tue, 22 Mar 2022 17:42:04 +0000 |
parents | 0920286a2d41 |
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<macros> <token name="@TOOL_VERSION@">2022</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> </requirements> </xml> <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token> <xml name="citations"> <citations> <citation type="doi">10.1016/j.softx.2015.06.001</citation> </citations> </xml> <xml name="md_inputs"> <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)"/> </when> <when value="default"> <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)"> <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"> <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"> <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> </param> <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" /> <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling"> <option value="true">Single coupling group (System)</option> <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option> </param> <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> <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." /> <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 simulation" value="0" min="0" help="MD steps" /> </when> </conditional> </xml> <xml name="log"> <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </xml> <xml name="maxwarn"> <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/> </xml> <xml name="log_outputs"> <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> <filter>capture_log</filter> </data> </xml> <xml name="xvg_or_tab"> <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file."> <option value="xvg">GROMACS XVG format</option> <option value="tabular" selected="true">Galaxy tabular</option> </param> </xml> <xml name="xvg_or_tab_outputs" token_name="" token_label=""> <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@"> <filter>fmt == 'xvg'</filter> </data> <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@"> <filter>fmt == 'tabular'</filter> </data> </xml> <xml name="test_params"> <param name="mdpfile" value="default" /> <param name="step_length" value="0.002"/> <param name="md_steps" value="500"/> <param name="write_freq" value="50"/> <param name="temperature" value="300"/> <param name="integrator" value="md" /> <param name="constraints" value="all-bonds"/> <param name="cutoffscheme" value="Verlet" /> <param name="coulombtype" value="PME" /> <param name="rlist" value="1.0" /> <param name="rcoulomb" value="1.0" /> <param name="rvdw" value="1.0" /> </xml> </macros>