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annotate energy.xml @ 3:b4a47b4ed264 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
author chemteam
date Tue, 21 Jan 2020 07:36:32 -0500
parents 5b0e6c2039a7
children 345c2a16b95f
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5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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1 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@VERSION@">
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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2 <description>from an energy (EDR) file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7 <expand macro="requirements" />
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9 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$edr_input' ./edr_input.edr &&
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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12 echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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13 ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg
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15 ]]></command>
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17 <inputs>
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18 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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19 <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated.">
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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20 <option value="1">Angle</option>
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21 <option value="2">Proper dihedrals</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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22 <option value="3">Ryckaert-Bellemans dihedrals</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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23 <option value="4">Lennard-Jones (1-4 interactions)</option>
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24 <option value="5">Coulomb (1-4 interactions)</option>
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25 <option value="6">Lennard-Jones energies (short range)</option>
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26 <option value="7">Dispersion correction</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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27 <option value="8">Coulomb (short range)</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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28 <option value="9">Reciprocal Coulomb energy</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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29 <option value="10" selected="True">Potential</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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30 <option value="11">Kinetic energy</option>
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31 <option value="12">Total energy</option>
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32 <option value="13">Temperature</option>
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33 <option value="14">Pressure DC</option>
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34 <option value="15">Pressure</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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35 <option value="16">Constr. RMSD</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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36 <option value="17">Box-X</option>
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37 <option value="18">Box-Y</option>
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38 <option value="19">Box-Z</option>
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39 <option value="20">Volume</option>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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40 <option value="21">Density</option>
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41 <option value="22">pV</option>
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42 <option value="23">Enthalpy</option>
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43 <option value="24">Virial(XX)</option>
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44 <option value="25">Virial(XY)</option>
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45 <option value="26">Virial(XZ)</option>
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46 <option value="27">Virial(YX)</option>
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47 <option value="28">Virial(YY)</option>
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48 <option value="29">Virial(YZ)</option>
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49 <option value="30">Virial(ZX)</option>
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50 <option value="31">Virial(ZY)</option>
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51 <option value="32">Virial(ZZ)</option>
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52 <option value="33">Pressure(XX)</option>
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53 <option value="34">Pressure(XY)</option>
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54 <option value="35">Pressure(XZ)</option>
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55 <option value="36">Pressure(YX)</option>
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56 <option value="37">Pressure(YY)</option>
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57 <option value="38">Pressure(YZ)</option>
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58 <option value="39">Pressure(ZX)</option>
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59 <option value="40">Pressure(ZY)</option>
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60 <option value="41">Pressure(ZZ)</option>
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61 <option value="42">Surface tension</option>
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62 <option value="43">Box-Vel-XX</option>
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63 <option value="44">Box-Vel-YY</option>
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64 <option value="45">Box-Vel-ZZ</option>
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65 <option value="46">Protein temperature</option>
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66 <option value="47">Non-protein temperature</option>
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67 <option value="48">Protein lambda values</option>
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68 <option value="49">Non-protein lambda values</option>
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69 </param>
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70
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71
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72 <expand macro="log" />
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73
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74 </inputs>
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75 <outputs>
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76 <data name="output1" format="xvg" from_work_dir="energy.xvg"/>
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77 <expand macro="log_outputs" />
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78 </outputs>
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79 <tests>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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80 <test>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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81 <param name="edr_input" value="md_0_1.edr" />
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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82 <param name="terms" value="10,12,13" />
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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83 <output name="output1" file="md_0_1.xvg" ftype="xvg" lines_diff="12"/>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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84 </test>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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85 </tests>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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86 <help><![CDATA[
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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87
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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88 .. class:: infomark
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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89
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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90 **What it does**
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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91
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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92 This tool extracts energy components from an energy (EDR) binary file. A list of terms to select is provided.
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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93
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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94 _____
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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95
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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96 .. class:: infomark
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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97
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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98 **Input**
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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99
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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100 - EDR binary file.
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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101 - Selection of terms to extract.
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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102
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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103 _____
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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104
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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105
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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106 .. class:: infomark
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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107
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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108 **Output**
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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109
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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110 - Tabular file containing selected terms and some header lines
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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111
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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112 ]]></help>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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113
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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114 <expand macro="citations" />
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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115 </tool>