annotate energy.xml @ 16:f26afd1b7104 draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author chemteam
date Mon, 24 Oct 2022 22:35:51 +0000
parents 593c63b5aff8
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1 <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <macros>
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3 <import>macros.xml</import>
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4 <token name="@GALAXY_VERSION@">1</token>
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5 </macros>
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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 '$edr_input' ./edr_input.edr &&
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12 echo -e '#echo str($terms).replace(',', '\\n')#'
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13 | gmx energy -f ./edr_input.edr -o ./energy.xvg >> verbose.txt 2>&1
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14 #if $fmt == 'tabular':
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15 &&
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16 grep '@\|#' energy.xvg &&
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17 grep -v '@\|#' energy.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > energy.tabular
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18 #end if
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19
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20 ]]></command>
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21
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22 <inputs>
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23 <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/>
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24 <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated.">
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25 <option value="Angle">Angle</option>
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26 <option value="Proper-Dih.">Proper dihedrals</option>
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27 <option value="Ryckaert-Bell.">Ryckaert-Bellemans dihedrals</option>
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28 <option value="LJ-14">Lennard-Jones (1-4 interactions)</option>
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29 <option value="Coulomb-14">Coulomb (1-4 interactions)</option>
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30 <option value="LJ-(SR)">Lennard-Jones energies (short range)</option>
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31 <option value="Disper.-corr.">Dispersion correction</option>
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32 <option value="Coulomb-(SR)">Coulomb (short range)</option>
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33 <option value="Coul.-recip.">Reciprocal Coulomb energy</option>
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34 <option value="Potential" selected="True">Potential energy</option>
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35 <option value="Kinetic-En.">Kinetic energy</option>
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36 <option value="Conserved-En.">Conserved energy</option>
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37 <option value="Total-Energy">Total energy</option>
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38 <option value="Temperature">Temperature</option>
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39 <option value="Pres.-DC">Pressure DC</option>
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40 <option value="Pressure">Pressure</option>
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41 <option value="Constr.-rmsd">Constr. RMSD</option>
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42 <option value="Box-X">Box-X</option>
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43 <option value="Box-Y">Box-Y</option>
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44 <option value="Box-Z">Box-Z</option>
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45 <option value="Volume">Volume</option>
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46 <option value="Density">Density</option>
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47 <option value="pV">pV</option>
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48 <option value="Enthalpy">Enthalpy</option>
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49 <option value="Vir-XX">Virial(XX)</option>
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50 <option value="Vir-XY">Virial(XY)</option>
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51 <option value="Vir-XZ">Virial(XZ)</option>
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52 <option value="Vir-YX">Virial(YX)</option>
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53 <option value="Vir-YY">Virial(YY)</option>
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54 <option value="Vir-YZ">Virial(YZ)</option>
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55 <option value="Vir-ZX">Virial(ZX)</option>
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56 <option value="Vir-ZY">Virial(ZY)</option>
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57 <option value="Vir-ZZ">Virial(ZZ)</option>
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58 <option value="Pres-XX">Pressure(XX)</option>
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59 <option value="Pres-XY">Pressure(XY)</option>
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60 <option value="Pres-XZ">Pressure(XZ)</option>
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61 <option value="Pres-YX">Pressure(YX)</option>
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62 <option value="Pres-YY">Pressure(YY)</option>
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63 <option value="Pres-YZ">Pressure(YZ)</option>
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64 <option value="Pres-ZX">Pressure(ZX)</option>
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65 <option value="Pres-ZY">Pressure(ZY)</option>
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66 <option value="Pres-ZZ">Pressure(ZZ)</option>
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67 <option value="#Surf*SurfTen">Surface tension</option>
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68 <option value="Box-Vel-XX">Box-Vel-XX</option>
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69 <option value="Box-Vel-YY">Box-Vel-YY</option>
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70 <option value="Box-Vel-ZZ">Box-Vel-ZZ</option>
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71 <option value="T-Protein">Protein temperature</option>
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72 <option value="T-non-Protein">Non-protein temperature</option>
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73 <option value="Lamb-Protein">Protein lambda values</option>
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74 <option value="Lamb-non-Protein">Non-protein lambda values</option>
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75 </param>
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76 <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file.">
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77 <option value="xvg">GROMACS XVG format</option>
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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78 <option value="tabular" selected="true">Galaxy tabular</option>
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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79 </param>
11
58c3e6711e94 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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80 <expand macro="xvg_or_tab" />
58c3e6711e94 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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81 <expand macro="log" />
0
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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82
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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83 </inputs>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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84 <outputs>
11
58c3e6711e94 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
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85 <expand macro="xvg_or_tab_outputs" name="energy" label="GROMACS energy components on ${on_string}"/>
0
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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86 <expand macro="log_outputs" />
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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87 </outputs>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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88 <tests>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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89 <test>
6
c8d2c0162b6e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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90 <param name="edr_input" value="outp.edr" />
14
593c63b5aff8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"
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91 <param name="terms" value="Potential,Total-Energy,Conserved-En." />
5
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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92 <param name="fmt" value="xvg" />
6
c8d2c0162b6e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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93 <output name="output1" file="outp.xvg" ftype="xvg" lines_diff="12"/>
0
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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94 </test>
5
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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95 <test>
6
c8d2c0162b6e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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96 <param name="edr_input" value="outp.edr" />
14
593c63b5aff8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"
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97 <param name="terms" value="Coul.-recip.,Kinetic-En.,Total-Energy" />
5
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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98 <param name="fmt" value="tabular" />
6
c8d2c0162b6e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
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99 <output name="output1" file="outp.tabular" ftype="tabular"/>
5
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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100 </test>
0
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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101 </tests>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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102 <help><![CDATA[
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 .. class:: infomark
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 **What it does**
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 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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109
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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110 _____
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 .. class:: infomark
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 **Input**
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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115
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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116 - EDR binary file.
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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117 - 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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118
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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119 _____
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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120
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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121
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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122 .. class:: infomark
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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123
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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124 **Output**
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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125
5
345c2a16b95f "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3846f6c5a15ba0586afbd5c901229e237a4e4f17"
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126 - Tabular or XVG file containing selected terms and some header lines
0
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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127
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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128 ]]></help>
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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129
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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130 <expand macro="citations" />
5b0e6c2039a7 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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131 </tool>