Mercurial > repos > chemteam > gmx_energy
comparison energy.xml @ 14:593c63b5aff8 draft
"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[ |