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comparison macros.xml @ 0:1a5960636405 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:48:44 -0400
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children ec3f665cca3e
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-1:000000000000 0:1a5960636405
1 <macros>
2 <token name="@VERSION@">2019.1.1</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="2019.1">gromacs</requirement>
6 </requirements>
7 </xml>
8 <xml name="citations">
9 <citations>
10 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
11 </citations>
12 </xml>
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
28 <conditional name="mdp">
29 <param name="mdpfile" type="select" label="Parameter input">
30 <option value="custom">Upload own MDP file</option>
31 <option value="default">Use default (partially customisable) setting</option>
32 </param>
33 <when value="custom">
34 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
35 </when>
36 <when value="default">
37 <param argument="integrator" type="select" label="Choice of integrator">
38 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
39 <option value="sd">Stochastic dynamics integrator</option>
40 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
41 </param>
42 <param argument="constraints" type="select" label="Bond constraints (constraints)">
43 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
44 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
45 <option value="all-bonds">All bonds (all-bonds).</option>
46 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
47 <option value="all-angles">All bonds and angles (all-angles).</option>
48 </param>
49 <param argument="cutoffscheme" type="select" label="Neighbor searching">
50 <option value="Verlet">Generate a pair list with buffering.</option>
51 <option value="group">Generate a pair list for groups of atoms.</option>
52 </param>
53 <param argument="coulombtype" type="select" label="Electrostatics">
54 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
55 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
56 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
57 </param>
58
59 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" />
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." />
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." />
62 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
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."/>
64 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
65 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
66
67 </when>
68
69 </conditional>
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
73
74 </xml>
75
76
77 <xml name="test_params">
78 <param name="mdpfile" value="default" />
79 <param name="step_length" value="0.002"/>
80 <param name="md_steps" value="500"/>
81 <param name="write_freq" value="50"/>
82 <param name="temperature" value="300"/>
83 <param name="integrator" value="md" />
84 <param name="constraints" value="all-bonds"/>
85 <param name="cutoffscheme" value="Verlet" />
86 <param name="coulombtype" value="PME" />
87 <param name="rlist" value="1.0" />
88 <param name="rcoulomb" value="1.0" />
89 <param name="rvdw" value="1.0" />
90 </xml>
91 </macros>