Mercurial > repos > chemteam > gmx_energy

changeset 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 b3ce2a978520
files energy.xml test-data/outp.tabular test-data/outp.xvg
diffstat 3 files changed, 72 insertions(+), 71 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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
@@ -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
--- 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
@@ -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)"