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comparison minim.xml @ 4:c1e98d48b8b4 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 12:48:06 -0400
parents ea7b9183bf30
children 6b79ed3d924d
comparison
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3:5ced6b7070b6 4:c1e98d48b8b4
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>