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comparison energy.xml @ 0:5b0e6c2039a7 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 11:14:03 -0500
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children 345c2a16b95f
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-1:000000000000 0:5b0e6c2039a7
1 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@VERSION@">
2 <description>from an energy (EDR) file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8
9 <command detect_errors="exit_code"><![CDATA[
10
11 ln -s '$edr_input' ./edr_input.edr &&
12 echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg
13 ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg
14
15 ]]></command>
16
17 <inputs>
18 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
19 <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated.">
20 <option value="1">Angle</option>
21 <option value="2">Proper dihedrals</option>
22 <option value="3">Ryckaert-Bellemans dihedrals</option>
23 <option value="4">Lennard-Jones (1-4 interactions)</option>
24 <option value="5">Coulomb (1-4 interactions)</option>
25 <option value="6">Lennard-Jones energies (short range)</option>
26 <option value="7">Dispersion correction</option>
27 <option value="8">Coulomb (short range)</option>
28 <option value="9">Reciprocal Coulomb energy</option>
29 <option value="10" selected="True">Potential</option>
30 <option value="11">Kinetic energy</option>
31 <option value="12">Total energy</option>
32 <option value="13">Temperature</option>
33 <option value="14">Pressure DC</option>
34 <option value="15">Pressure</option>
35 <option value="16">Constr. RMSD</option>
36 <option value="17">Box-X</option>
37 <option value="18">Box-Y</option>
38 <option value="19">Box-Z</option>
39 <option value="20">Volume</option>
40 <option value="21">Density</option>
41 <option value="22">pV</option>
42 <option value="23">Enthalpy</option>
43 <option value="24">Virial(XX)</option>
44 <option value="25">Virial(XY)</option>
45 <option value="26">Virial(XZ)</option>
46 <option value="27">Virial(YX)</option>
47 <option value="28">Virial(YY)</option>
48 <option value="29">Virial(YZ)</option>
49 <option value="30">Virial(ZX)</option>
50 <option value="31">Virial(ZY)</option>
51 <option value="32">Virial(ZZ)</option>
52 <option value="33">Pressure(XX)</option>
53 <option value="34">Pressure(XY)</option>
54 <option value="35">Pressure(XZ)</option>
55 <option value="36">Pressure(YX)</option>
56 <option value="37">Pressure(YY)</option>
57 <option value="38">Pressure(YZ)</option>
58 <option value="39">Pressure(ZX)</option>
59 <option value="40">Pressure(ZY)</option>
60 <option value="41">Pressure(ZZ)</option>
61 <option value="42">Surface tension</option>
62 <option value="43">Box-Vel-XX</option>
63 <option value="44">Box-Vel-YY</option>
64 <option value="45">Box-Vel-ZZ</option>
65 <option value="46">Protein temperature</option>
66 <option value="47">Non-protein temperature</option>
67 <option value="48">Protein lambda values</option>
68 <option value="49">Non-protein lambda values</option>
69 </param>
70
71
72 <expand macro="log" />
73
74 </inputs>
75 <outputs>
76 <data name="output1" format="xvg" from_work_dir="energy.xvg"/>
77 <expand macro="log_outputs" />
78 </outputs>
79 <tests>
80 <test>
81 <param name="edr_input" value="md_0_1.edr" />
82 <param name="terms" value="10,12,13" />
83 <output name="output1" file="md_0_1.xvg" ftype="xvg" lines_diff="12"/>
84 </test>
85 </tests>
86 <help><![CDATA[
87
88 .. class:: infomark
89
90 **What it does**
91
92 This tool extracts energy components from an energy (EDR) binary file. A list of terms to select is provided.
93
94 _____
95
96 .. class:: infomark
97
98 **Input**
99
100 - EDR binary file.
101 - Selection of terms to extract.
102
103 _____
104
105
106 .. class:: infomark
107
108 **Output**
109
110 - Tabular file containing selected terms and some header lines
111
112 ]]></help>
113
114 <expand macro="citations" />
115 </tool>