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comparison solvate.xml @ 17:9a1e472aa515 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 04ccbbe525c43164b061fe738500a84d73f89afa"
author chemteam
date Mon, 08 Nov 2021 18:40:42 +0000
parents 97b2c06ae168
children 2dfcf594c838
comparison
equal deleted inserted replaced
16:61094e01eff9 17:9a1e472aa515
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[
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 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 @MAXWARN_CMD@ &>> 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 -seed $seed &>> 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
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 <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." />
58 58
59 <expand macro="maxwarn" />
59 <expand macro="log" /> 60 <expand macro="log" />
60 61
61 </inputs> 62 </inputs>
62 <outputs> 63 <outputs>
63 <data name="output1" format="gro" from_work_dir="solv.gro" label="GROMACS solvation (GRO) on ${on_string}"/> 64 <data name="output1" format="gro" from_work_dir="solv.gro" label="GROMACS solvation (GRO) on ${on_string}"/>