<?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: [Preparation]-->
<tool id="AddMissingAtoms" name="AddMissingAtoms" version="1.1.0">
  <description>add missing atoms to protein structures</description>
  <macros>
    <token name="@EXECUTABLE@">AddMissingAtoms</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>AddMissingAtoms

#if $param_i:
  -i $param_i
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_opt_hyd:
  -opt_hyd $param_opt_hyd
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
    <param name="param_opt_hyd" type="integer" min="0" max="1" optional="True" value="0" label="optimize the positions of hydrogens" help="(-opt_hyd) "/>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" format="pdb"/>
  </outputs>
  <help>AddMissingAtoms tool allows you to missing atoms, i.e. hydrogens to a protein structure.

 Optional parameter is the optimize_hydrogens flag (-opt_hyd), which uses the AMBER force field to run a quick energy minization for all hydrogen atoms.

Output of this tool is one pdb-file containing the input protein structure with added atoms.

</help>
</tool>