Mercurial > repos > chemteam > gmx_setup

comparison macros.xml @ 6:c7bcae9fe040 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:16:14 -0500
parents 35b314fe6c90
children cf03bccaa325
comparison
equal deleted inserted replaced
5:35b314fe6c90 6:c7bcae9fe040
1 <macros> 1 <macros>
2 <token name="@VERSION@">2019.1.2</token> 2 <token name="@VERSION@">2019.1.3</token>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.1">gromacs</requirement> 5 <requirement type="package" version="2019.1">gromacs</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
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
28 <conditional name="mdp"> 15 <conditional name="mdp">
29 <param name="mdpfile" type="select" label="Parameter input"> 16 <param name="mdpfile" type="select" label="Parameter input">
30 <option value="custom">Upload own MDP file</option> 17 <option value="custom">Upload own MDP file</option>
31 <option value="default">Use default (partially customisable) setting</option> 18 <option value="default">Use default (partially customisable) setting</option>
71 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> 58 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
72 59
73 60
74 </xml> 61 </xml>
75 62
63 <xml name="log">
64 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
65 </xml>
66
67 <xml name="log_outputs">
68 <data name="report" format="txt" from_work_dir="verbose.txt">
69 <filter>capture_log</filter>
70 </data>
71 </xml>
76 72
77 <xml name="test_params"> 73 <xml name="test_params">
78 <param name="mdpfile" value="default" /> 74 <param name="mdpfile" value="default" />
79 <param name="step_length" value="0.002"/> 75 <param name="step_length" value="0.002"/>
80 <param name="md_steps" value="500"/> 76 <param name="md_steps" value="500"/>