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comparison energy.xml @ 14:593c63b5aff8 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"
author chemteam
date Tue, 22 Mar 2022 17:42:04 +0000
parents 0920286a2d41
children
comparison
equal deleted inserted replaced
13:0920286a2d41 14:593c63b5aff8
1 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 <token name="@GALAXY_VERSION@">0</token> 4 <token name="@GALAXY_VERSION@">1</token>
5 </macros> 5 </macros>
6 6
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 ln -s '$edr_input' ./edr_input.edr && 11 ln -s '$edr_input' ./edr_input.edr &&
12 echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg 12 echo -e '#echo str($terms).replace(',', '\\n')#'
13 ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg 13 | gmx energy -f ./edr_input.edr -o ./energy.xvg >> verbose.txt 2>&1
14 #if $fmt == 'tabular': 14 #if $fmt == 'tabular':
15 && 15 &&
16 grep '@\|#' energy.xvg && 16 grep '@\|#' energy.xvg &&
17 grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > energy.tabular 17 grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > energy.tabular
18 #end if 18 #end if
20 ]]></command> 20 ]]></command>
21 21
22 <inputs> 22 <inputs>
23 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/> 23 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
24 <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated."> 24 <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated.">
25 <option value="1">Angle</option> 25 <option value="Angle">Angle</option>
26 <option value="2">Proper dihedrals</option> 26 <option value="Proper-Dih.">Proper dihedrals</option>
27 <option value="3">Ryckaert-Bellemans dihedrals</option> 27 <option value="Ryckaert-Bell.">Ryckaert-Bellemans dihedrals</option>
28 <option value="4">Lennard-Jones (1-4 interactions)</option> 28 <option value="LJ-14">Lennard-Jones (1-4 interactions)</option>
29 <option value="5">Coulomb (1-4 interactions)</option> 29 <option value="Coulomb-14">Coulomb (1-4 interactions)</option>
30 <option value="6">Lennard-Jones energies (short range)</option> 30 <option value="LJ-(SR)">Lennard-Jones energies (short range)</option>
31 <option value="7">Dispersion correction</option> 31 <option value="Disper.-corr.">Dispersion correction</option>
32 <option value="8">Coulomb (short range)</option> 32 <option value="Coulomb-(SR)">Coulomb (short range)</option>
33 <option value="9">Reciprocal Coulomb energy</option> 33 <option value="Coul.-recip.">Reciprocal Coulomb energy</option>
34 <option value="10" selected="True">Potential</option> 34 <option value="Potential" selected="True">Potential energy</option>
35 <option value="11">Kinetic energy</option> 35 <option value="Kinetic-En.">Kinetic energy</option>
36 <option value="12">Total energy</option> 36 <option value="Conserved-En.">Conserved energy</option>
37 <option value="13">Temperature</option> 37 <option value="Total-Energy">Total energy</option>
38 <option value="14">Pressure DC</option> 38 <option value="Temperature">Temperature</option>
39 <option value="15">Pressure</option> 39 <option value="Pres.-DC">Pressure DC</option>
40 <option value="16">Constr. RMSD</option> 40 <option value="Pressure">Pressure</option>
41 <option value="17">Box-X</option> 41 <option value="Constr.-rmsd">Constr. RMSD</option>
42 <option value="18">Box-Y</option> 42 <option value="Box-X">Box-X</option>
43 <option value="19">Box-Z</option> 43 <option value="Box-Y">Box-Y</option>
44 <option value="20">Volume</option> 44 <option value="Box-Z">Box-Z</option>
45 <option value="21">Density</option> 45 <option value="Volume">Volume</option>
46 <option value="22">pV</option> 46 <option value="Density">Density</option>
47 <option value="23">Enthalpy</option> 47 <option value="pV">pV</option>
48 <option value="24">Virial(XX)</option> 48 <option value="Enthalpy">Enthalpy</option>
49 <option value="25">Virial(XY)</option> 49 <option value="Vir-XX">Virial(XX)</option>
50 <option value="26">Virial(XZ)</option> 50 <option value="Vir-XY">Virial(XY)</option>
51 <option value="27">Virial(YX)</option> 51 <option value="Vir-XZ">Virial(XZ)</option>
52 <option value="28">Virial(YY)</option> 52 <option value="Vir-YX">Virial(YX)</option>
53 <option value="29">Virial(YZ)</option> 53 <option value="Vir-YY">Virial(YY)</option>
54 <option value="30">Virial(ZX)</option> 54 <option value="Vir-YZ">Virial(YZ)</option>
55 <option value="31">Virial(ZY)</option> 55 <option value="Vir-ZX">Virial(ZX)</option>
56 <option value="32">Virial(ZZ)</option> 56 <option value="Vir-ZY">Virial(ZY)</option>
57 <option value="33">Pressure(XX)</option> 57 <option value="Vir-ZZ">Virial(ZZ)</option>
58 <option value="34">Pressure(XY)</option> 58 <option value="Pres-XX">Pressure(XX)</option>
59 <option value="35">Pressure(XZ)</option> 59 <option value="Pres-XY">Pressure(XY)</option>
60 <option value="36">Pressure(YX)</option> 60 <option value="Pres-XZ">Pressure(XZ)</option>
61 <option value="37">Pressure(YY)</option> 61 <option value="Pres-YX">Pressure(YX)</option>
62 <option value="38">Pressure(YZ)</option> 62 <option value="Pres-YY">Pressure(YY)</option>
63 <option value="39">Pressure(ZX)</option> 63 <option value="Pres-YZ">Pressure(YZ)</option>
64 <option value="40">Pressure(ZY)</option> 64 <option value="Pres-ZX">Pressure(ZX)</option>
65 <option value="41">Pressure(ZZ)</option> 65 <option value="Pres-ZY">Pressure(ZY)</option>
66 <option value="42">Surface tension</option> 66 <option value="Pres-ZZ">Pressure(ZZ)</option>
67 <option value="43">Box-Vel-XX</option> 67 <option value="#Surf*SurfTen">Surface tension</option>
68 <option value="44">Box-Vel-YY</option> 68 <option value="Box-Vel-XX">Box-Vel-XX</option>
69 <option value="45">Box-Vel-ZZ</option> 69 <option value="Box-Vel-YY">Box-Vel-YY</option>
70 <option value="46">Protein temperature</option> 70 <option value="Box-Vel-ZZ">Box-Vel-ZZ</option>
71 <option value="47">Non-protein temperature</option> 71 <option value="T-Protein">Protein temperature</option>
72 <option value="48">Protein lambda values</option> 72 <option value="T-non-Protein">Non-protein temperature</option>
73 <option value="49">Non-protein lambda values</option> 73 <option value="Lamb-Protein">Protein lambda values</option>
74 <option value="Lamb-non-Protein">Non-protein lambda values</option>
74 </param> 75 </param>
75 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file."> 76 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
76 <option value="xvg">GROMACS XVG format</option> 77 <option value="xvg">GROMACS XVG format</option>
77 <option value="tabular" selected="true">Galaxy tabular</option> 78 <option value="tabular" selected="true">Galaxy tabular</option>
78 </param> 79 </param>
85 <expand macro="log_outputs" /> 86 <expand macro="log_outputs" />
86 </outputs> 87 </outputs>
87 <tests> 88 <tests>
88 <test> 89 <test>
89 <param name="edr_input" value="outp.edr" /> 90 <param name="edr_input" value="outp.edr" />
90 <param name="terms" value="10,12,13" /> 91 <param name="terms" value="Potential,Total-Energy,Conserved-En." />
91 <param name="fmt" value="xvg" /> 92 <param name="fmt" value="xvg" />
92 <output name="output1" file="outp.xvg" ftype="xvg" lines_diff="12"/> 93 <output name="output1" file="outp.xvg" ftype="xvg" lines_diff="12"/>
93 </test> 94 </test>
94 <test> 95 <test>
95 <param name="edr_input" value="outp.edr" /> 96 <param name="edr_input" value="outp.edr" />
96 <param name="terms" value="10,12,13" /> 97 <param name="terms" value="Coul.-recip.,Kinetic-En.,Total-Energy" />
97 <param name="fmt" value="tabular" /> 98 <param name="fmt" value="tabular" />
98 <output name="output1" file="outp.tabular" ftype="tabular"/> 99 <output name="output1" file="outp.tabular" ftype="tabular"/>
99 </test> 100 </test>
100 </tests> 101 </tests>
101 <help><![CDATA[ 102 <help><![CDATA[