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comparison macros.xml @ 10:3f50a097ff35 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit c428519a27419b62de0556f5beecc4bb7c187ad0"
author chemteam
date Tue, 30 Nov 2021 15:29:51 +0000
parents 54eadeb47ab9
children f9dd1349d76d
comparison
equal deleted inserted replaced
9:54eadeb47ab9 10:3f50a097ff35
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement> 5 <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8
9 <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token> 8 <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>
10 9
11 <xml name="citations"> 10 <xml name="citations">
12 <citations> 11 <citations>
13 <citation type="doi">10.1016/j.softx.2015.06.001</citation> 12 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
43 <param argument="coulombtype" type="select" label="Electrostatics"> 42 <param argument="coulombtype" type="select" label="Electrostatics">
44 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option> 43 <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
45 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option> 44 <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
46 <option value="Reaction-Field-zero">Reaction field electrostatics.</option> 45 <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
47 </param> 46 </param>
48 47 <param name="temperature" type="integer" label="Temperature (K)" value="0" min="0" max="1000000" help="Temperature" />
49 <param argument="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>
50 <param argument="step_length" type="float" label="Step length in ps" value="0" min="0.0001" max="1.0" help="Step length in ps." /> 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." />
51 <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." /> 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." />
52 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/> 54 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
53 <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."/> 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."/>
54 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/> 56 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
55 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" /> 57 <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" help="MD steps" />
56 58
57 </when> 59 </when>
58 60
59 </conditional> 61 </conditional>
60 62
65 </xml> 67 </xml>
66 68
67 <xml name="maxwarn"> 69 <xml name="maxwarn">
68 <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."/> 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."/>
69 </xml> 71 </xml>
72
70 73
71 <xml name="log_outputs"> 74 <xml name="log_outputs">
72 <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}"> 75 <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
73 <filter>capture_log</filter> 76 <filter>capture_log</filter>
74 </data> 77 </data>