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comparison macros.xml @ 0:26467f738ed4 draft

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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
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-1:000000000000 0:26467f738ed4
1 <macros>
2 <token name="@TOOL_VERSION@">2022</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
6 </requirements>
7 </xml>
8 <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>
9
10 <xml name="citations">
11 <citations>
12 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
13 </citations>
14 </xml>
15 <xml name="md_inputs">
16
17 <conditional name="mdp">
18 <param name="mdpfile" type="select" label="Parameter input">
19 <option value="custom">Upload own MDP file</option>
20 <option value="default">Use default (partially customisable) setting</option>
21 </param>
22 <when value="custom">
23 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
24 </when>
25 <when value="default">
26 <param argument="integrator" type="select" label="Choice of integrator">
27 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
28 <option value="sd">Stochastic dynamics integrator</option>
29 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
30 </param>
31 <param argument="constraints" type="select" label="Bond constraints (constraints)">
32 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
33 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
34 <option value="all-bonds">All bonds (all-bonds).</option>
35 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
36 <option value="all-angles">All bonds and angles (all-angles).</option>
37 </param>
38 <param argument="cutoffscheme" type="select" label="Neighbor searching">
39 <option value="Verlet">Generate a pair list with buffering.</option>
40 <option value="group">Generate a pair list for groups of atoms.</option>
41 </param>
42 <param argument="coulombtype" type="select" label="Electrostatics">
43 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
44 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
45 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
46 </param>
47 <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" />
48 <param name="systemTcouple" type="select" label="Number of groups to set for thermocoupling">
49 <option value="true">Single coupling group (System)</option>
50 <option value="false" selected="true">Two coupling groups (Protein and Non-Protein)</option>
51 </param>
52 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." />
53 <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." />
54 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
55 <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."/>
56 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
57 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" />
58
59 </when>
60
61 </conditional>
62
63 </xml>
64
65 <xml name="log">
66 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
67 </xml>
68
69 <xml name="maxwarn">
70 <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."/>
71 </xml>
72
73
74 <xml name="log_outputs">
75 <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
76 <filter>capture_log</filter>
77 </data>
78 </xml>
79
80 <xml name="xvg_or_tab">
81 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
82 <option value="xvg">GROMACS XVG format</option>
83 <option value="tabular" selected="true">Galaxy tabular</option>
84 </param>
85 </xml>
86
87 <xml name="xvg_or_tab_outputs" token_name="" token_label="">
88 <data name="output1" format="xvg" from_work_dir="@NAME@.xvg" label="@LABEL@">
89 <filter>fmt == 'xvg'</filter>
90 </data>
91 <data name="output2" format="tabular" from_work_dir="@NAME@.tabular" label="@LABEL@">
92 <filter>fmt == 'tabular'</filter>
93 </data>
94 </xml>
95
96 <xml name="test_params">
97 <param name="mdpfile" value="default" />
98 <param name="step_length" value="0.002"/>
99 <param name="md_steps" value="500"/>
100 <param name="write_freq" value="50"/>
101 <param name="temperature" value="300"/>
102 <param name="integrator" value="md" />
103 <param name="constraints" value="all-bonds"/>
104 <param name="cutoffscheme" value="Verlet" />
105 <param name="coulombtype" value="PME" />
106 <param name="rlist" value="1.0" />
107 <param name="rcoulomb" value="1.0" />
108 <param name="rvdw" value="1.0" />
109 </xml>
110 </macros>