Mercurial > repos > chemteam > gmx_solvate
diff solvate.xml @ 3:7161b230adad draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
---|---|
date | Mon, 07 Oct 2019 12:47:31 -0400 |
parents | 77aaf9a68166 |
children | cdacad684da1 |
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--- a/solvate.xml Fri Aug 30 15:03:34 2019 -0400 +++ b/solvate.xml Mon Oct 07 12:47:31 2019 -0400 @@ -37,14 +37,14 @@ </configfile> </configfiles> <inputs> - <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> - <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> - <param name="water_model" type="select" label="Water model for solvation."> + <param argument="gro_input" type="data" format='gro' label="GRO structure file"/> + <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> + <param name="water_model" type="select" label="Water model for solvation"> <option value="tip3p">TIP3P</option> <option value="tip4p">TIP4P</option> <option value="spc216">SPC</option> </param> - <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> + <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> </inputs> <outputs> @@ -65,7 +65,31 @@ </tests> <help><![CDATA[ -Select a water model - consistent with the one selected in system set-up and provide GRO and TOP files to be updated with the added water molecules. In addition, sodium or chloride ions are added if necessary to ensure the system is charge-neutral. +.. class:: infomark + +**What it does** + +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. + +_____ + +.. class:: infomark + +**Input** + + - GRO structure file. + - Topology (TOP) file. + +In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup. + +_____ + + +.. class:: infomark + +**Output** + + - GRO structure file. ]]></help>