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annotate macros.xml @ 12:4da9ee404eab draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:03:07 -0400
parents 8b2553f4f114
children 2c349b027a01
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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1 <macros>
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2 <token name="@TOOL_VERSION@">2020.2</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="citations">
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9 <citations>
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10 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
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11 </citations>
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12 </xml>
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13 <xml name="md_inputs">
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15 <conditional name="mdp">
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16 <param name="mdpfile" type="select" label="Parameter input">
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17 <option value="custom">Upload own MDP file</option>
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18 <option value="default">Use default (partially customisable) setting</option>
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19 </param>
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20 <when value="custom">
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21 <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
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22 </when>
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23 <when value="default">
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24 <param argument="integrator" type="select" label="Choice of integrator">
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25 <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
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26 <option value="sd">Stochastic dynamics integrator</option>
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27 <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
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28 </param>
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29 <param argument="constraints" type="select" label="Bond constraints (constraints)">
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30 <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
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31 <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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32 <option value="all-bonds">All bonds (all-bonds).</option>
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33 <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
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34 <option value="all-angles">All bonds and angles (all-angles).</option>
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35 </param>
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36 <param argument="cutoffscheme" type="select" label="Neighbor searching">
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37 <option value="Verlet">Generate a pair list with buffering.</option>
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38 <option value="group">Generate a pair list for groups of atoms.</option>
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39 </param>
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40 <param argument="coulombtype" type="select" label="Electrostatics">
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41 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
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42 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
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43 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
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44 </param>
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46 <param argument="temperature" type="integer" label="Temperature /K" value="0" min="0" max="1000000" help="Temperature" />
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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." />
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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." />
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49 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
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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."/>
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51 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
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52 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
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54 </when>
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56 </conditional>
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58 </xml>
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60 <xml name="log">
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61 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
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62 </xml>
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64 <xml name="log_outputs">
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65 <data name="report" format="txt" from_work_dir="verbose.txt">
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66 <filter>capture_log</filter>
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67 </data>
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68 </xml>
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70 <xml name="test_params">
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71 <param name="mdpfile" value="default" />
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72 <param name="step_length" value="0.002"/>
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73 <param name="md_steps" value="500"/>
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74 <param name="write_freq" value="50"/>
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75 <param name="temperature" value="300"/>
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76 <param name="integrator" value="md" />
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77 <param name="constraints" value="all-bonds"/>
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78 <param name="cutoffscheme" value="Verlet" />
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79 <param name="coulombtype" value="PME" />
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80 <param name="rlist" value="1.0" />
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81 <param name="rcoulomb" value="1.0" />
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82 <param name="rvdw" value="1.0" />
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83 </xml>
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84 </macros>