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comparison galaxy_stubs/CalculateSolvationFreeEnergy.xml @ 2:605370bc1def draft default tip

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ForceFields]-->
4 <tool id="CalculateSolvationFreeEnergy" name="CalculateSolvationFreeEnergy" version="1.1.0">
5 <description>calculate solvation free energy of a protein using AMBER </description>
6 <macros>
7 <token name="@EXECUTABLE@">CalculateSolvationFreeEnergy</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="stdio"/>
11 <expand macro="requirements"/>
12 <command>CalculateSolvationFreeEnergy
13
14 #if $param_pdb:
15 -pdb $param_pdb
16 #end if
17 #if $param_epsilon_medium:
18 -epsilon_medium $param_epsilon_medium
19 #end if
20 #if $param_epsilon_vacuum:
21 -epsilon_vacuum $param_epsilon_vacuum
22 #end if
23 </command>
24 <inputs>
25 <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
26 <param name="param_epsilon_medium" type="float" value="0.0" label="dielectric constant in medium" help="(-epsilon_medium) "/>
27 <param name="param_epsilon_vacuum" type="float" value="1.0" label="dielectric constant in vacuum" help="(-epsilon_vacuum) "/>
28 </inputs>
29 <expand macro="advanced_options"/>
30 <outputs>
31 <data name="param_stdout" format="text" label="Output from stdout"/>
32 </outputs>
33 <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).
34
35 </help>
36 </tool>