<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
<tool id="proteinprotonator" name="ProteinProtonator" version="1.0.1">
    <description>protonate protein structures</description>
    <command interpreter="bash"><![CDATA[../../ProteinProtonator 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ph ) != ''  and str( $ph ) != 'None' :
   -ph "$ph"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input file" type="data" format="pdb"/>
        <param name="ph" optional="true" label="Optional: pH-value for pH-dep. protonation" type="text" area="true" size="1x5" value="7.0"/>
    </inputs>
    <outputs>
        <data name="o" format="pdb" format_source="i"/>
    </outputs>
    <help>ProteinProtonator allows you add hydrogens to a protein structure.

Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed.

Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help>
</tool>