Mercurial > repos > chemteam > gmx_solvate

comparison solvate.xml @ 11:27ea4e1a3f95 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 12:57:49 -0400
parents 645139abefae
children e205c82e9959
comparison
equal deleted inserted replaced
10:dc2400b6361d 11:27ea4e1a3f95
1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@VERSION@"> 1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>to structure and topology files</description> 2 <description>to structure and topology files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
5 </macros> 6 </macros>
6 7
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
8 9
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt 16 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt
16 17
17 #if $neutralise == "true": 18 #if $neutralise == "true":
18 && 19 &&
19 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt && 20 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt &&
20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt && 21 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc $conc &>> verbose.txt &&
21 mv solv_ions.gro solv.gro 22 mv solv_ions.gro solv.gro
22 #end if 23 #end if
23 24
24 25
25 ]]></command> 26 ]]></command>
26 <configfiles> 27 <configfiles>
27 <!-- .mdp file for the gromacs simulation --> 28 <!-- .mdp file for the gromacs simulation -->
28 <configfile name="ions"> 29 <configfile name="ions">
29 : Parameters are not so important here as no simulation is run 30
31 ; Parameters are not so important here as no simulation is run
30 integrator = steep 32 integrator = steep
31 emtol = 1000.0 33 emtol = 1000.0
32 emstep = 0.01 34 emstep = 0.01
33 nsteps = 1 35 nsteps = 1
34 nstlist = 1 36 nstlist = 1
51 <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it."> 53 <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.">
52 <option value="true">Yes, add ions</option> 54 <option value="true">Yes, add ions</option>
53 <option value="false">No</option> 55 <option value="false">No</option>
54 </param> 56 </param>
55 57
58 <param argument="conc" type="float" value="0" min="0" max="6" label="Specify salt concentration (sodium chloride) to add, in mol/liter" help="Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules." />
59
56 <expand macro="log" /> 60 <expand macro="log" />
57 61
58 </inputs> 62 </inputs>
59 <outputs> 63 <outputs>
60 <data name="output1" format="gro" from_work_dir="solv.gro"/> 64 <data name="output1" format="gro" from_work_dir="solv.gro"/>
65 <test> 69 <test>
66 <param name="gro_input" value="newbox.gro" /> 70 <param name="gro_input" value="newbox.gro" />
67 <param name="neutralise" value="true" /> 71 <param name="neutralise" value="true" />
68 <param name="top_input" value="topol.top" /> 72 <param name="top_input" value="topol.top" />
69 <param name="water_model" value="spc216" /> 73 <param name="water_model" value="spc216" />
74 <param name="conc" value="1" />
70 <output name="output1" ftype="gro"> 75 <output name="output1" ftype="gro">
71 <!-- replacement of water with ions is random, thus we cannot compare the whole file --> 76 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
72 <assert_contents> 77 <assert_contents>
73 <has_text text="1.014 5.822 2.833"/> 78 <has_text text="1.671 1.591 3.533"/>
74 <has_text text="6.831 5.961 6.119"/> 79 <has_text text="2.032 2.417 1.345"/>
75 <has_text text="3.592 6.520 5.241"/> 80 <has_text text="3.438 1.662 0.307"/>
81 <has_text text="2218CL"/>
82 <has_text text="2147NA"/>
76 </assert_contents> 83 </assert_contents>
77 </output> 84 </output>
78 <output name="output2" file="topol_solv.top" ftype="top"/> 85 <output name="output2" file="topol_solv.top" ftype="top" lines_diff="4">
86 <assert_contents>
87 <has_line line="SOL 2130" />
88 <has_line line="NA 41" />
89 <has_line line="CL 43" />
90 </assert_contents>
91 </output>
79 </test> 92 </test>
80 <test> 93 <test>
81 <param name="gro_input" value="newbox.gro" /> 94 <param name="gro_input" value="newbox.gro" />
82 <param name="neutralise" value="false" /> 95 <param name="neutralise" value="false" />
83 <param name="top_input" value="topol.top" /> 96 <param name="top_input" value="topol.top"/>
84 <param name="water_model" value="spc216" /> 97 <param name="water_model" value="spc216" />
85 <output name="output1" file="solv.gro" ftype="gro"/> 98 <param name="conc" value="0" />
99 <output name="output1" ftype="gro">
100 <assert_contents>
101 <has_text text="1.671 1.591 3.533"/>
102 <has_text text="2.032 2.417 1.345"/>
103 <has_text text="3.438 1.662 0.307"/>
104 <not_has_text text="2218CL"/>
105 </assert_contents>
106 </output>
86 </test> 107 </test>
87 </tests> 108 </tests>
88 <help><![CDATA[ 109 <help><![CDATA[
89 110
90 .. class:: infomark 111 .. class:: infomark
91 112
92 **What it does** 113 **What it does**
93 114
94 This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions will be added if necessary to ensure the system is charge-neutral. 115 This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions can be added if necessary to ensure the system is charge-neutral.
95 116
96 _____ 117 _____
97 118
98 .. class:: infomark 119 .. class:: infomark
99 120