Mercurial > repos > luis > ball
diff galaxy_stubs/CalculateSolvationFreeEnergy.xml @ 2:605370bc1def draft default tip
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| author | luis |
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| date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/CalculateSolvationFreeEnergy.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,36 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [ForceFields]--> +<tool id="CalculateSolvationFreeEnergy" name="CalculateSolvationFreeEnergy" version="1.1.0"> + <description>calculate solvation free energy of a protein using AMBER </description> + <macros> + <token name="@EXECUTABLE@">CalculateSolvationFreeEnergy</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>CalculateSolvationFreeEnergy + +#if $param_pdb: + -pdb $param_pdb +#end if +#if $param_epsilon_medium: + -epsilon_medium $param_epsilon_medium +#end if +#if $param_epsilon_vacuum: + -epsilon_vacuum $param_epsilon_vacuum +#end if +</command> + <inputs> + <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/> + <param name="param_epsilon_medium" type="float" value="0.0" label="dielectric constant in medium" help="(-epsilon_medium) "/> + <param name="param_epsilon_vacuum" type="float" value="1.0" label="dielectric constant in vacuum" help="(-epsilon_vacuum) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool computes the solvation free energy of a pdb file using the Jackson-Sternberg approach (bonded energy using a force field and a non bonded energy (electrostatics only) by solving the Poisson-Boltzmann equation. Parameters are the dielectric constants for the medium (-epsilon_medium) and the vacuum (-epsilon_vacuum). + +</help> +</tool>