| Previous changeset 13:0920286a2d41 (2022-03-14) Next changeset 15:b3ce2a978520 (2022-07-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587" |
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modified:
energy.xml test-data/outp.tabular test-data/outp.xvg |
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| diff -r 0920286a2d41 -r 593c63b5aff8 energy.xml --- a/energy.xml Mon Mar 14 10:39:42 2022 +0000 +++ b/energy.xml Tue Mar 22 17:42:04 2022 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <tool id="gmx_energy" name="Extract energy components with GROMACS" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements" /> @@ -9,8 +9,8 @@ <command detect_errors="exit_code"><![CDATA[ ln -s '$edr_input' ./edr_input.edr && - echo #echo str($terms).replace(',', ' ')# | gmx energy -f ./edr_input.edr -o ./energy.xvg - ## echo #echo ' '.join(str($terms).split(','))# | gmx energy -f ./edr_input.edr -o ./energy.xvg + echo -e '#echo str($terms).replace(',', '\\n')#' + | gmx energy -f ./edr_input.edr -o ./energy.xvg >> verbose.txt 2>&1 #if $fmt == 'tabular': && grep '@\|#' energy.xvg && @@ -22,55 +22,56 @@ <inputs> <param argument="edr_input" type="data" format="edr" label="EDR file" help="GROMACS energy binary file"/> <param argument="terms" type='select' label="Terms to calculate" multiple="true" help="Select terms for which values should be calculated."> - <option value="1">Angle</option> - <option value="2">Proper dihedrals</option> - <option value="3">Ryckaert-Bellemans dihedrals</option> - <option value="4">Lennard-Jones (1-4 interactions)</option> - <option value="5">Coulomb (1-4 interactions)</option> - <option value="6">Lennard-Jones energies (short range)</option> - <option value="7">Dispersion correction</option> - <option value="8">Coulomb (short range)</option> - <option value="9">Reciprocal Coulomb energy</option> - <option value="10" selected="True">Potential</option> - <option value="11">Kinetic energy</option> - <option value="12">Total energy</option> - <option value="13">Temperature</option> - <option value="14">Pressure DC</option> - <option value="15">Pressure</option> - <option value="16">Constr. RMSD</option> - <option value="17">Box-X</option> - <option value="18">Box-Y</option> - <option value="19">Box-Z</option> - <option value="20">Volume</option> - <option value="21">Density</option> - <option value="22">pV</option> - <option value="23">Enthalpy</option> - <option value="24">Virial(XX)</option> - <option value="25">Virial(XY)</option> - <option value="26">Virial(XZ)</option> - <option value="27">Virial(YX)</option> - <option value="28">Virial(YY)</option> - <option value="29">Virial(YZ)</option> - <option value="30">Virial(ZX)</option> - <option value="31">Virial(ZY)</option> - <option value="32">Virial(ZZ)</option> - <option value="33">Pressure(XX)</option> - <option value="34">Pressure(XY)</option> - <option value="35">Pressure(XZ)</option> - <option value="36">Pressure(YX)</option> - <option value="37">Pressure(YY)</option> - <option value="38">Pressure(YZ)</option> - <option value="39">Pressure(ZX)</option> - <option value="40">Pressure(ZY)</option> - <option value="41">Pressure(ZZ)</option> - <option value="42">Surface tension</option> - <option value="43">Box-Vel-XX</option> - <option value="44">Box-Vel-YY</option> - <option value="45">Box-Vel-ZZ</option> - <option value="46">Protein temperature</option> - <option value="47">Non-protein temperature</option> - <option value="48">Protein lambda values</option> - <option value="49">Non-protein lambda values</option> + <option value="Angle">Angle</option> + <option value="Proper-Dih.">Proper dihedrals</option> + <option value="Ryckaert-Bell.">Ryckaert-Bellemans dihedrals</option> + <option value="LJ-14">Lennard-Jones (1-4 interactions)</option> + <option value="Coulomb-14">Coulomb (1-4 interactions)</option> + <option value="LJ-(SR)">Lennard-Jones energies (short range)</option> + <option value="Disper.-corr.">Dispersion correction</option> + <option value="Coulomb-(SR)">Coulomb (short range)</option> + <option value="Coul.-recip.">Reciprocal Coulomb energy</option> + <option value="Potential" selected="True">Potential energy</option> + <option value="Kinetic-En.">Kinetic energy</option> + <option value="Conserved-En.">Conserved energy</option> + <option value="Total-Energy">Total energy</option> + <option value="Temperature">Temperature</option> + <option value="Pres.-DC">Pressure DC</option> + <option value="Pressure">Pressure</option> + <option value="Constr.-rmsd">Constr. RMSD</option> + <option value="Box-X">Box-X</option> + <option value="Box-Y">Box-Y</option> + <option value="Box-Z">Box-Z</option> + <option value="Volume">Volume</option> + <option value="Density">Density</option> + <option value="pV">pV</option> + <option value="Enthalpy">Enthalpy</option> + <option value="Vir-XX">Virial(XX)</option> + <option value="Vir-XY">Virial(XY)</option> + <option value="Vir-XZ">Virial(XZ)</option> + <option value="Vir-YX">Virial(YX)</option> + <option value="Vir-YY">Virial(YY)</option> + <option value="Vir-YZ">Virial(YZ)</option> + <option value="Vir-ZX">Virial(ZX)</option> + <option value="Vir-ZY">Virial(ZY)</option> + <option value="Vir-ZZ">Virial(ZZ)</option> + <option value="Pres-XX">Pressure(XX)</option> + <option value="Pres-XY">Pressure(XY)</option> + <option value="Pres-XZ">Pressure(XZ)</option> + <option value="Pres-YX">Pressure(YX)</option> + <option value="Pres-YY">Pressure(YY)</option> + <option value="Pres-YZ">Pressure(YZ)</option> + <option value="Pres-ZX">Pressure(ZX)</option> + <option value="Pres-ZY">Pressure(ZY)</option> + <option value="Pres-ZZ">Pressure(ZZ)</option> + <option value="#Surf*SurfTen">Surface tension</option> + <option value="Box-Vel-XX">Box-Vel-XX</option> + <option value="Box-Vel-YY">Box-Vel-YY</option> + <option value="Box-Vel-ZZ">Box-Vel-ZZ</option> + <option value="T-Protein">Protein temperature</option> + <option value="T-non-Protein">Non-protein temperature</option> + <option value="Lamb-Protein">Protein lambda values</option> + <option value="Lamb-non-Protein">Non-protein lambda values</option> </param> <param argument="fmt" type='select' label="Output format" help="Format for output; either standard GROMACS XVG, or Galaxy tabular file."> <option value="xvg">GROMACS XVG format</option> @@ -87,13 +88,13 @@ <tests> <test> <param name="edr_input" value="outp.edr" /> - <param name="terms" value="10,12,13" /> + <param name="terms" value="Potential,Total-Energy,Conserved-En." /> <param name="fmt" value="xvg" /> <output name="output1" file="outp.xvg" ftype="xvg" lines_diff="12"/> </test> <test> <param name="edr_input" value="outp.edr" /> - <param name="terms" value="10,12,13" /> + <param name="terms" value="Coul.-recip.,Kinetic-En.,Total-Energy" /> <param name="fmt" value="tabular" /> <output name="output1" file="outp.tabular" ftype="tabular"/> </test> |
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| diff -r 0920286a2d41 -r 593c63b5aff8 test-data/outp.tabular --- a/test-data/outp.tabular Mon Mar 14 10:39:42 2022 +0000 +++ b/test-data/outp.tabular Tue Mar 22 17:42:04 2022 +0000 |
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| @@ -1,11 +1,11 @@ -0.000000 -875.856201 -565.607910 -561.483948 -0.100000 -937.817383 -652.096558 -563.097961 -0.200000 -1076.080811 -764.079712 -564.585632 -0.300000 -1128.099854 -869.548645 -563.387207 -0.400000 -1194.588623 -941.101868 -563.371216 -0.500000 -1229.046509 -942.665039 -564.364685 -0.600000 -1304.865845 -1042.604736 -565.530396 -0.700000 -1355.996216 -1110.028687 -566.059509 -0.800000 -1339.003906 -1115.218750 -566.635681 -0.900000 -1310.706909 -1073.441406 -566.569702 -1.000000 -1306.671997 -1089.731323 -566.253174 +0.000000 615.943726 310.248291 -565.607910 +0.100000 546.932983 285.720825 -652.096558 +0.200000 455.540436 312.001129 -764.079712 +0.300000 399.011078 258.551208 -869.548645 +0.400000 375.411926 253.486740 -941.101868 +0.500000 341.939514 286.381439 -942.665039 +0.600000 311.339386 262.261047 -1042.604736 +0.700000 267.376160 245.967499 -1110.028687 +0.800000 281.326874 223.785217 -1115.218750 +0.900000 272.021881 237.265472 -1073.441406 +1.000000 304.201172 216.940704 -1089.731323 |
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| diff -r 0920286a2d41 -r 593c63b5aff8 test-data/outp.xvg --- a/test-data/outp.xvg Mon Mar 14 10:39:42 2022 +0000 +++ b/test-data/outp.xvg Tue Mar 22 17:42:04 2022 +0000 |
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| @@ -1,15 +1,15 @@ -# This file was created Mon Jun 7 09:13:14 2021 +# This file was created Mon Mar 21 18:17:18 2022 # Created by: -# :-) GROMACS - gmx energy, 2021.1-MODIFIED (-: +# :-) GROMACS - gmx energy, 2022-conda_forge (-: # -# Executable: /home/runner/miniconda3/envs/__gromacs@2021.1/bin.AVX2_256/gmx -# Data prefix: /home/runner/miniconda3/envs/__gromacs@2021.1 -# Working dir: /tmp/tmpc3_9dc8m/job_working_directory/000/13/working +# Executable: /home/simon/miniconda3/envs/__gromacs@2022/bin.AVX2_256/gmx +# Data prefix: /home/simon/miniconda3/envs/__gromacs@2022 +# Working dir: /tmp/tmpt1cctsw0/job_working_directory/000/2/working # Command line: # gmx energy -f ./edr_input.edr -o ./energy.xvg # gmx energy is part of G R O M A C S: # -# Glycine aRginine prOline Methionine Alanine Cystine Serine +# Green Red Orange Magenta Azure Cyan Skyblue # @ title "GROMACS Energies" @ xaxis label "Time (ps)" |