<!--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="pocketcutter" name="PocketCutter" version="1.5">
    <description>cut binding pocket surface</description>
    <command interpreter="bash"><![CDATA[../../PocketCutter 
#if str( $rec ) != ''  and str( $rec ) != 'None' :
   -rec "$rec"
#end if
#if str( $rl ) != ''  and str( $rl ) != 'None' :
   -rl "$rl"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $ini ) != ''  and str( $ini ) != 'None' :
   -ini "$ini"
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="rec" optional="false" label="receptor pdb-file" type="data" format="pdb"/>
        <param name="rl" optional="true" label="reference ligand" type="data" format="mol2/sdf/drf"/>
        <param name="ini" optional="true" label="input ini file" type="data" format="ini"/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf"/>
    </outputs>
    <help>This tools selects all atoms from a given protein structure that form part of the binding pocket's SES surface.

The location and size of the binding pocket can be obtained from either a given reference ligand or an ini file that contains a description as generated by the PocketDetector tool, or both.

The output of this tool is a molecule file that contain just the selected surface atoms and can be used e.g. with SurfaceMatcher.</help>
</tool>