Mercurial > repos > chemteam > gmx_check
diff macros.xml @ 0:26467f738ed4 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
| author | chemteam |
|---|---|
| date | Tue, 12 Jul 2022 12:48:09 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 12 12:48:09 2022 +0000 @@ -0,0 +1,110 @@ +<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>