Mercurial > repos > chemteam > gmx_em
comparison minim.xml @ 4:c1e98d48b8b4 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:48:06 -0400 |
parents | ea7b9183bf30 |
children | 6b79ed3d924d |
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3:5ced6b7070b6 | 4:c1e98d48b8b4 |
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45 </configfiles> | 45 </configfiles> |
46 | 46 |
47 <inputs> | 47 <inputs> |
48 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> | 48 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> |
49 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> | 49 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> |
50 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
51 | |
52 <conditional name="mdp"> | 50 <conditional name="mdp"> |
53 <param name="mdpfile" type="select" label="Parameter input"> | 51 <param name="mdpfile" type="select" label="Parameter input"> |
54 <option value="custom">Upload own MDP file</option> | 52 <option value="custom">Upload own MDP file</option> |
55 <option value="default">Use default (partially customisable) setting</option> | 53 <option value="default">Use default (partially customisable) setting</option> |
56 </param> | 54 </param> |
79 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> | 77 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" /> |
80 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> | 78 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" /> |
81 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> | 79 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." /> |
82 </when> | 80 </when> |
83 </conditional> | 81 </conditional> |
82 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
84 </inputs> | 83 </inputs> |
85 <outputs> | 84 <outputs> |
86 <data name="output1" format="gro" from_work_dir="em.gro"/> | 85 <data name="output1" format="gro" from_work_dir="em.gro"/> |
87 <data name="report" format="txt" from_work_dir="verbose.txt"> | 86 <data name="report" format="txt" from_work_dir="verbose.txt"> |
88 <filter>capture_log</filter> | 87 <filter>capture_log</filter> |
113 </test> | 112 </test> |
114 | 113 |
115 </tests> | 114 </tests> |
116 <help><![CDATA[ | 115 <help><![CDATA[ |
117 | 116 |
118 Upload GRO and TOP files for energy minimisation. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options. | 117 .. class:: infomark |
118 | |
119 **What it does** | |
120 | |
121 This tool performs energy minimization of a system prior to a GROMACS simulation. | |
122 | |
123 _____ | |
124 | |
125 .. class:: infomark | |
126 | |
127 **Input** | |
128 | |
129 - GRO structure file. | |
130 - Topology (TOP) file. | |
131 - MDP parameter file (optional) | |
132 | |
133 To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options. | |
134 | |
135 .. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html | |
136 | |
137 _____ | |
138 | |
139 | |
140 .. class:: infomark | |
141 | |
142 **Output** | |
143 | |
144 - GRO structure file. | |
119 | 145 |
120 ]]></help> | 146 ]]></help> |
121 | 147 |
122 <expand macro="citations" /> | 148 <expand macro="citations" /> |
123 </tool> | 149 </tool> |