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comparison solvate.xml @ 5:645139abefae draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:10:25 -0500
parents cdacad684da1
children 27ea4e1a3f95
comparison
equal deleted inserted replaced
4:cdacad684da1 5:645139abefae
10 10
11 ln -s '$ions' ./ions.mdp && 11 ln -s '$ions' ./ions.mdp &&
12 ln -s '$gro_input' ./gro_input.gro && 12 ln -s '$gro_input' ./gro_input.gro &&
13 ln -s '$top_input' ./top_input.top && 13 ln -s '$top_input' ./top_input.top &&
14 14
15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && 15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt
16 16
17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt && 17 #if $neutralise == "true":
18 &&
19 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 mv solv_ions.gro solv.gro
22 #end if
18 23
19 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt 24
20
21 ]]></command> 25 ]]></command>
22 <configfiles> 26 <configfiles>
23 <!-- .mdp file for the gromacs simulation --> 27 <!-- .mdp file for the gromacs simulation -->
24 <configfile name="ions"> 28 <configfile name="ions">
25 : Parameters are not so important here as no simulation is run 29 : Parameters are not so important here as no simulation is run
42 <param name="water_model" type="select" label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water."> 46 <param name="water_model" type="select" label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water.">
43 <option value="spc216" selected="true">SPC (generic three-point model)</option> 47 <option value="spc216" selected="true">SPC (generic three-point model)</option>
44 <option value="tip4p">TIP4P (four-point model)</option> 48 <option value="tip4p">TIP4P (four-point model)</option>
45 <option value="tip5p">TIP5P (five-point model)</option> 49 <option value="tip5p">TIP5P (five-point model)</option>
46 </param> 50 </param>
47 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> 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.">
52 <option value="true">Yes, add ions</option>
53 <option value="false">No</option>
54 </param>
55
56 <expand macro="log" />
48 57
49 </inputs> 58 </inputs>
50 <outputs> 59 <outputs>
51 <data name="output1" format="gro" from_work_dir="solv_ions.gro"/> 60 <data name="output1" format="gro" from_work_dir="solv.gro"/>
52 <data name="output2" format="top" from_work_dir="./top_input.top"/> 61 <data name="output2" format="top" from_work_dir="./top_input.top"/>
53 <data name="report" format="txt" from_work_dir="verbose.txt"> 62 <expand macro="log_outputs" />
54 <filter>capture_log</filter>
55 </data>
56 </outputs> 63 </outputs>
57 <tests> 64 <tests>
58 <test> 65 <test>
59 <param name="gro_input" value="newbox.gro" /> 66 <param name="gro_input" value="newbox.gro" />
67 <param name="neutralise" value="true" />
60 <param name="top_input" value="topol.top" /> 68 <param name="top_input" value="topol.top" />
61 <param name="water_model" value="spc216" /> 69 <param name="water_model" value="spc216" />
62 <output name="output1" file="solv_ions.gro" ftype="gro" compare="sim_size"/> 70 <output name="output1" ftype="gro">
71 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
72 <assert_contents>
73 <has_text text="1.014 5.822 2.833"/>
74 <has_text text="6.831 5.961 6.119"/>
75 <has_text text="3.592 6.520 5.241"/>
76 </assert_contents>
77 </output>
63 <output name="output2" file="topol_solv.top" ftype="top"/> 78 <output name="output2" file="topol_solv.top" ftype="top"/>
79 </test>
80 <test>
81 <param name="gro_input" value="newbox.gro" />
82 <param name="neutralise" value="false" />
83 <param name="top_input" value="topol.top" />
84 <param name="water_model" value="spc216" />
85 <output name="output1" file="solv.gro" ftype="gro"/>
64 </test> 86 </test>
65 </tests> 87 </tests>
66 <help><![CDATA[ 88 <help><![CDATA[
67 89
68 .. class:: infomark 90 .. class:: infomark