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comparison solvate.xml @ 12:e205c82e9959 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
author chemteam
date Tue, 20 Oct 2020 10:43:39 +0000
parents 27ea4e1a3f95
children ae87e7b2454c
comparison
equal deleted inserted replaced
11:27ea4e1a3f95 12:e205c82e9959
1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_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 <token name="@GALAXY_VERSION@">1</token>
6 </macros> 6 </macros>
7 7
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
12 ln -s '$ions' ./ions.mdp && 12 ln -s '$ions' ./ions.mdp &&
13 ln -s '$gro_input' ./gro_input.gro && 13 ln -s '$gro_input' ./gro_input.gro &&
14 ln -s '$top_input' ./top_input.top && 14 ln -s '$top_input' ./top_input.top &&
15 15
16 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 &&
17 17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt
18 #if $neutralise == "true": 18 #if $neutralise and $conc: ## else this step would do nothing
19 && 19 &&
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 $neutralise -conc $conc &>> 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 &&
22 mv solv_ions.gro solv.gro 21 mv solv_ions.gro solv.gro
23 #end if 22 #end if
24
25 23
26 ]]></command> 24 ]]></command>
27 <configfiles> 25 <configfiles>
28 <!-- .mdp file for the gromacs simulation --> 26 <!-- .mdp file for the gromacs simulation -->
29 <configfile name="ions"> 27 <configfile name="ions">
49 <option value="spc216" selected="true">SPC (generic three-point model)</option> 47 <option value="spc216" selected="true">SPC (generic three-point model)</option>
50 <option value="tip4p">TIP4P (four-point model)</option> 48 <option value="tip4p">TIP4P (four-point model)</option>
51 <option value="tip5p">TIP5P (five-point model)</option> 49 <option value="tip5p">TIP5P (five-point model)</option>
52 </param> 50 </param>
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."> 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.">
54 <option value="true">Yes, add ions</option> 52 <option value="-neutral">Yes, add ions</option>
55 <option value="false">No</option> 53 <option value="">No</option>
56 </param> 54 </param>
57 55
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." /> 56 <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 57
60 <expand macro="log" /> 58 <expand macro="log" />
66 <expand macro="log_outputs" /> 64 <expand macro="log_outputs" />
67 </outputs> 65 </outputs>
68 <tests> 66 <tests>
69 <test> 67 <test>
70 <param name="gro_input" value="newbox.gro" /> 68 <param name="gro_input" value="newbox.gro" />
71 <param name="neutralise" value="true" /> 69 <param name="neutralise" value="-neutral" />
72 <param name="top_input" value="topol.top" /> 70 <param name="top_input" value="topol.top" />
73 <param name="water_model" value="spc216" /> 71 <param name="water_model" value="spc216" />
74 <param name="conc" value="1" /> 72 <param name="conc" value="1" />
75 <output name="output1" ftype="gro"> 73 <output name="output1" ftype="gro">
76 <!-- replacement of water with ions is random, thus we cannot compare the whole file --> 74 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
90 </assert_contents> 88 </assert_contents>
91 </output> 89 </output>
92 </test> 90 </test>
93 <test> 91 <test>
94 <param name="gro_input" value="newbox.gro" /> 92 <param name="gro_input" value="newbox.gro" />
95 <param name="neutralise" value="false" /> 93 <param name="neutralise" value="" />
96 <param name="top_input" value="topol.top"/> 94 <param name="top_input" value="topol.top"/>
97 <param name="water_model" value="spc216" /> 95 <param name="water_model" value="spc216" />
98 <param name="conc" value="0" /> 96 <param name="conc" value="0" />
99 <output name="output1" ftype="gro"> 97 <output name="output1" ftype="gro">
100 <assert_contents> 98 <assert_contents>