view galaxy_stubs/CalculateEnergy.xml @ 2:605370bc1def draft default tip

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<?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="CalculateEnergy" name="CalculateEnergy" version="1.1.0">
  <description>calculate free energy of a protein </description>
  <macros>
    <token name="@EXECUTABLE@">CalculateEnergy</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>CalculateEnergy

#if $param_pdb:
  -pdb $param_pdb
#end if
#if $param_force_field:
  -force_field
  #if " " in str($param_force_field):
    "$param_force_field"
  #else
    $param_force_field
  #end if
#end if
#if $param_non_bond_cutoff:
  -non_bond_cutoff $param_non_bond_cutoff
#end if
#if $param_elec_stat_cuton:
  -elec_stat_cuton $param_elec_stat_cuton
#end if
#if $param_elec_stat_cutoff:
  -elec_stat_cutoff $param_elec_stat_cutoff
#end if
#if $param_dist_dep_dielec:
  -dist_dep_dielec $param_dist_dep_dielec
#end if
#if $param_overwrite_types:
  -overwrite_types $param_overwrite_types
#end if
#if $param_overwrite_charges:
  -overwrite_charges $param_overwrite_charges
#end if
</command>
  <inputs>
    <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
    <param name="param_force_field" type="select" optional="True" value="AMBER" label="force field (AMBER, MMFF94)" help="(-force_field) ">
      <option value="AMBER">AMBER</option>
      <option value=" MMFF94"> MMFF94</option>
    </param>
    <param name="param_non_bond_cutoff" type="float" value="20.0" label="cutoff radius in calculations of nonbonded interactions" help="(-non_bond_cutoff) "/>
    <param name="param_elec_stat_cuton" type="float" value="13.0" label="electrostatic cuton" help="(-elec_stat_cuton) "/>
    <param name="param_elec_stat_cutoff" type="float" value="15.0" label="electrostatic cutoff" help="(-elec_stat_cutoff) "/>
    <param name="param_dist_dep_dielec" type="integer" min="0" max="1" optional="True" value="0" label="apply distance dependent dielectric constant" help="(-dist_dep_dielec) "/>
    <param name="param_overwrite_types" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-empty type names" help="(-overwrite_types) "/>
    <param name="param_overwrite_charges" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-zero charges" help="(-overwrite_charges) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <help>This tool computes the free energy of a pdb file using a specified force field (-force_field) and force field parameters (-non_bond_cutoff, -elec_stat_cuton ... ).

</help>
</tool>