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comparison macros.xml @ 3:7161b230adad 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 12:47:31 -0400
parents b37a1d7bf6c2
children cdacad684da1
comparison
equal deleted inserted replaced
2:b37a1d7bf6c2 3:7161b230adad
1 <macros> 1 <macros>
2 <token name="@VERSION@">2019.1</token> 2 <token name="@VERSION@">2019.1.1</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@VERSION@">gromacs</requirement> 5 <requirement type="package" version="2019.1">gromacs</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <xml name="citations"> 8 <xml name="citations">
9 <citations> 9 <citations>
10 <citation type="doi">10.1016/j.softx.2015.06.001</citation> 10 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
11 </citations> 11 </citations>
12 </xml> 12 </xml>
13 <xml name="md_inputs"> 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
14 <conditional name="mdp"> 28 <conditional name="mdp">
15 <param name="mdpfile" type="select" label="Parameter input"> 29 <param name="mdpfile" type="select" label="Parameter input">
16 <option value="custom">Upload own MDP file</option> 30 <option value="custom">Upload own MDP file</option>
17 <option value="default">Use default (partially customisable) setting</option> 31 <option value="default">Use default (partially customisable) setting</option>
18 </param> 32 </param>
19 <when value="custom"> 33 <when value="custom">
20 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/> 34 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
21 </when> 35 </when>
22 <when value="default"> 36 <when value="default">
23 <param argument="integrator" type="select" label="Choice of integrator."> 37 <param argument="integrator" type="select" label="Choice of integrator">
24 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option> 38 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
25 <option value="sd">Stochastic dynamics integrator</option> 39 <option value="sd">Stochastic dynamics integrator</option>
26 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option> 40 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
27 </param> 41 </param>
28 <param argument="constraints" type="select" label="Bond constraints (constraints)."> 42 <param argument="constraints" type="select" label="Bond constraints (constraints)">
29 <option value="none">No constraints except for those defined explicitly in the topology (none).</option> 43 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
30 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option> 44 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
31 <option value="all-bonds">All bonds (all-bonds).</option> 45 <option value="all-bonds">All bonds (all-bonds).</option>
32 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option> 46 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
33 <option value="all-angles">All bonds and angles (all-angles).</option> 47 <option value="all-angles">All bonds and angles (all-angles).</option>
34 </param> 48 </param>
35 <param argument="cutoffscheme" type="select" label="Neighbor searching."> 49 <param argument="cutoffscheme" type="select" label="Neighbor searching">
36 <option value="Verlet">Generate a pair list with buffering.</option> 50 <option value="Verlet">Generate a pair list with buffering.</option>
37 <option value="group">Generate a pair list for groups of atoms.</option> 51 <option value="group">Generate a pair list for groups of atoms.</option>
38 </param> 52 </param>
39 <param argument="coulombtype" type="select" label="Electrostatics."> 53 <param argument="coulombtype" type="select" label="Electrostatics">
40 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> 54 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
41 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> 55 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
42 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> 56 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
43 </param> 57 </param>
44 58
46 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> 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." />
47 <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." /> 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." />
48 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> 62 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
49 <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."/> 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."/>
50 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> 64 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
51 <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" /> 65 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
52 66
53 </when> 67 </when>
54 68
55 </conditional> 69 </conditional>
56
57 <param argument="traj" type="select" label="Trajectory output.">
58 <option value='none'>Return no trajectory output</option>
59 <option value='xtc'>Return .xtc file (reduced precision)</option>
60 <option value='trr'>Return .trr file (full precision)</option>
61 <option value='both'>Return both .xtc and .trr files</option>
62 </param>
63 70
64 <param argument="str" type="select" label="Structure output."> 71 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
65 <option value='none'>Return no trajectory output</option>
66 <option value='gro'>Return .gro file</option>
67 <option value='pdb'>Return .pdb file</option>
68 <option value='both'>Return both .gro and .pdb files</option>
69 </param>
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 72
73 73
74 </xml> 74 </xml>
75 75
76 76