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comparison macros.xml @ 0:644ca8dfdf28 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
author chemteam
date Thu, 04 Oct 2018 17:39:10 -0400
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children acc9922f3eab
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-1:000000000000 0:644ca8dfdf28
1 <macros>
2 <token name="@VERSION@">2018.2</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">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
14
15 <xml name="md_inputs">
16 <conditional name="mdp">
17 <param name="mdpfile" type="select" label="Parameter input">
18 <option value="custom">Upload own MDP file</option>
19 <option value="default">Use default (partially customisable) setting</option>
20 </param>
21 <when value="custom">
22 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/>
23 </when>
24 <when value="default">
25 <param argument="integrator" type="select" label="Choice of integrator.">
26 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
27 <option value="sd">Stochastic dynamics integrator</option>
28 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
29 </param>
30 <param argument="constraints" type="select" label="Bond constraints (constraints).">
31 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
32 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
33 <option value="all-bonds">All bonds (all-bonds).</option>
34 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
35 <option value="all-angles">All bonds and angles (all-angles).</option>
36 </param>
37 <param argument="cutoffscheme" type="select" label="Neighbor searching.">
38 <option value="Verlet">Generate a pair list with buffering.</option>
39 <option value="group">Generate a pair list for groups of atoms.</option>
40 </param>
41 <param argument="coulombtype" type="select" label="Electrostatics.">
42 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
43 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
44 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
45 </param>
46
47 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" />
48 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
49 <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." />
50 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
51 <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."/>
52 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
53 <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" />
54
55 </when>
56
57 </conditional>
58
59 <param argument="traj" type="select" label="Trajectory output.">
60 <option value='none'>Return no trajectory output</option>
61 <option value='xtc'>Return .xtc file (reduced precision)</option>
62 <option value='trr'>Return .trr file (full precision)</option>
63 <option value='both'>Return both .xtc and .trr files</option>
64 </param>
65
66 <param argument="str" type="select" label="Structure output.">
67 <option value='none'>Return no trajectory output</option>
68 <option value='gro'>Return .gro file</option>
69 <option value='pdb'>Return .pdb file</option>
70 <option value='both'>Return both .gro and .pdb files</option>
71 </param>
72
73 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
74
75
76 </xml>
77
78
79 <xml name="test_params">
80 <param name="mdpfile" value="default" />
81 <param name="step_length" value="0.002"/>
82 <param name="md_steps" value="500"/>
83 <param name="write_freq" value="50"/>
84 <param name="temperature" value="300"/>
85 <param name="integrator" value="md" />
86 <param name="constraints" value="all-bonds"/>
87 <param name="cutoffscheme" value="Verlet" />
88 <param name="coulombtype" value="PME" />
89 <param name="rlist" value="1.0" />
90 <param name="rcoulomb" value="1.0" />
91 <param name="rvdw" value="1.0" />
92 </xml>
93 </macros>