Mercurial > repos > chemteam > gmx_solvate
comparison solvate.xml @ 15:97b2c06ae168 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"
author | chemteam |
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date | Wed, 29 Sep 2021 07:40:34 +0000 |
parents | 2c8ed1b52bf7 |
children | 9a1e472aa515 |
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14:2c8ed1b52bf7 | 15:97b2c06ae168 |
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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@">1</token> | 5 <token name="@GALAXY_VERSION@">0</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[ |
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 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt | 17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt |
18 #if $neutralise or $conc: ## else this step would do nothing | 18 #if $neutralise or $conc: ## else this step would do nothing |
19 && | 19 && |
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 && | 20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc -seed $seed &>> verbose.txt && |
21 mv solv_ions.gro solv.gro | 21 mv solv_ions.gro solv.gro |
22 #end if | 22 #end if |
23 | 23 |
24 ]]></command> | 24 ]]></command> |
25 <configfiles> | 25 <configfiles> |
52 <option value="-neutral">Yes, add ions</option> | 52 <option value="-neutral">Yes, add ions</option> |
53 <option value="">No</option> | 53 <option value="">No</option> |
54 </param> | 54 </param> |
55 | 55 |
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." /> | 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." /> |
57 <param argument="seed" type="integer" value="1" min="0" label="Random seed for adding ions" help="Select a random seed for replacing solvent with ions. Set to 0 to generate a seed." /> | |
57 | 58 |
58 <expand macro="log" /> | 59 <expand macro="log" /> |
59 | 60 |
60 </inputs> | 61 </inputs> |
61 <outputs> | 62 <outputs> |
62 <data name="output1" format="gro" from_work_dir="solv.gro"/> | 63 <data name="output1" format="gro" from_work_dir="solv.gro" label="GROMACS solvation (GRO) on ${on_string}"/> |
63 <data name="output2" format="top" from_work_dir="./top_input.top"/> | 64 <data name="output2" format="top" from_work_dir="./top_input.top" label="GROMACS solvation (TOP) on ${on_string}"/> |
64 <expand macro="log_outputs" /> | 65 <expand macro="log_outputs" /> |
65 </outputs> | 66 </outputs> |
66 <tests> | 67 <tests> |
67 <test> | 68 <test> |
68 <param name="gro_input" value="newbox.gro" /> | 69 <param name="gro_input" value="newbox.gro" /> |
69 <param name="neutralise" value="-neutral" /> | 70 <param name="neutralise" value="-neutral" /> |
70 <param name="top_input" value="topol.top" /> | 71 <param name="top_input" value="topol.top" /> |
71 <param name="water_model" value="spc216" /> | 72 <param name="water_model" value="spc216" /> |
72 <param name="conc" value="1" /> | 73 <param name="conc" value="1" /> |
73 <output name="output1" ftype="gro"> | 74 <output name="output1" ftype="gro"> |
74 <!-- replacement of water with ions is random, thus we cannot compare the whole file --> | 75 <!-- file is big, thus we do not compare the whole file --> |
75 <assert_contents> | 76 <assert_contents> |
76 <has_text text="1.671 1.591 3.533"/> | 77 <has_text text="1.671 1.591 3.533"/> |
77 <has_text text="2.032 2.417 1.345"/> | 78 <has_text text="2.032 2.417 1.345"/> |
78 <has_text text="3.438 1.662 0.307"/> | 79 <has_text text="3.438 1.662 0.307"/> |
79 <has_text text="2218CL"/> | 80 <has_text text="2218CL"/> |
80 <has_text text="2147NA"/> | 81 <has_text text="2147NA"/> |
81 </assert_contents> | 82 </assert_contents> |
82 </output> | 83 </output> |
83 <output name="output2" file="topol_solv.top" ftype="top" lines_diff="4"> | 84 <output name="output2" ftype="top"> |
84 <assert_contents> | 85 <assert_contents> |
85 <has_line line="SOL 2130" /> | 86 <has_line line="SOL 2130" /> |
86 <has_line line="NA 41" /> | 87 <has_line line="NA 41" /> |
87 <has_line line="CL 43" /> | 88 <has_line line="CL 43" /> |
88 </assert_contents> | 89 </assert_contents> |