<!--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="pdbcutter" name="PDBCutter" version="1.6">
    <description>separate ligand and receptor</description>
    <command interpreter="bash"><![CDATA[../../PDBCutter 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $rec ) != ''  and str( $rec ) != 'None' :
   -rec "$rec"
#end if
#if str( $lig ) != ''  and str( $lig ) != 'None' :
   -lig "$lig"
#end if
#if str( $lig_chain ) != ''  and str( $lig_chain ) != 'None' :
   -lig_chain "$lig_chain"
#end if
#if str( $lig_name ) != ''  and str( $lig_name ) != 'None' :
   -lig_name "$lig_name"
#end if
#if str( $rm_ch ) != ''  and str( $rm_ch ) != 'None' :
   -rm_ch "$rm_ch"
#end if
#if str( $id ) != ''  and str( $id ) != 'None' :
   -id "$id"
#end if
#if str( $p ) != ''  and str( $p ) != 'None' :
   -p "$p"
#end if
#if str( $rm_res ) != ''  and str( $rm_res ) != 'None' :
   -rm_res "$rm_res"
#end if
#if str( $auto ) != ''  and str( $auto ) != 'None' :
   -auto
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input pdb-file" type="data" format="pdb"/>
        <param name="lig_chain" optional="false" label="chain-name of ligand" area="true" type="text" size="1x15"/>
        <param name="lig_name" optional="false" label="ligand name" area="true" type="text" size="1x15"/>
        <param name="rm_ch" optional="true" label="Optional: protein chains that are to be deleted" area="true" type="text" size="1x15"/>
        <param name="id" optional="true" label="Optional: PDB ID for download of ligand as sdf from PDB server, if desired" area="true" type="text" size="1x15"/>
        <param name="p" optional="true" label="Optional: proxy for ligand download, if required" area="true" type="text" size="1x15"/>
        <param name="rm_res" optional="true" label="Optional: pdb-residues that are to be deleted (e.g. water or ions)" area="true" type="text" size="1x15"/>
        <param name="auto" optional="true" label="extract largest heterosystem as ligand (ignore specified lig. def.)" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="rec" format="pdb"/>
        <data name="lig" format="pdb"/>
    </outputs>
    <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.

The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
If desired, the correct topology of the reference ligand can be downloaded by this tool from the Protein Data Bank as an sd-file and stored in the specified ligand output file.
Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.

Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one file containing the reference ligand.</help>
</tool>