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comparison macros.xml @ 0:72c2b7992c26 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:14:52 -0500
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children e6907ad8ff76
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-1:000000000000 0:72c2b7992c26
1 <macros>
2 <token name="@VERSION@">2019.1.3</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
15 <conditional name="mdp">
16 <param name="mdpfile" type="select" label="Parameter input">
17 <option value="custom">Upload own MDP file</option>
18 <option value="default">Use default (partially customisable) setting</option>
19 </param>
20 <when value="custom">
21 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
22 </when>
23 <when value="default">
24 <param argument="integrator" type="select" label="Choice of integrator">
25 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
26 <option value="sd">Stochastic dynamics integrator</option>
27 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
28 </param>
29 <param argument="constraints" type="select" label="Bond constraints (constraints)">
30 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
31 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
32 <option value="all-bonds">All bonds (all-bonds).</option>
33 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
34 <option value="all-angles">All bonds and angles (all-angles).</option>
35 </param>
36 <param argument="cutoffscheme" type="select" label="Neighbor searching">
37 <option value="Verlet">Generate a pair list with buffering.</option>
38 <option value="group">Generate a pair list for groups of atoms.</option>
39 </param>
40 <param argument="coulombtype" type="select" label="Electrostatics">
41 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
42 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
43 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
44 </param>
45
46 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" />
47 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
48 <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." />
49 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
50 <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."/>
51 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
52 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
53
54 </when>
55
56 </conditional>
57
58 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
59
60
61 </xml>
62
63 <xml name="log">
64 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
65 </xml>
66
67 <xml name="log_outputs">
68 <data name="report" format="txt" from_work_dir="verbose.txt">
69 <filter>capture_log</filter>
70 </data>
71 </xml>
72
73 <xml name="test_params">
74 <param name="mdpfile" value="default" />
75 <param name="step_length" value="0.002"/>
76 <param name="md_steps" value="500"/>
77 <param name="write_freq" value="50"/>
78 <param name="temperature" value="300"/>
79 <param name="integrator" value="md" />
80 <param name="constraints" value="all-bonds"/>
81 <param name="cutoffscheme" value="Verlet" />
82 <param name="coulombtype" value="PME" />
83 <param name="rlist" value="1.0" />
84 <param name="rcoulomb" value="1.0" />
85 <param name="rvdw" value="1.0" />
86 </xml>
87 </macros>