<!--This is a configuration file for the integration of a BALLSuite 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="bondassigner" name="BOA Constructor" version="0.9.6" force_history_refresh="True"> 
		<description>computes bond order assignments for a ligand</description>
		<command>/usr/local/ballaxy/build/BondOrderAssigner 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $outfile ) != ''  and str( $outfile ) != 'None' :
   -o "$outfile"
#end if
#if str( $outfile.id ) != '' and str( $outfile.id ) != 'None' :
	-o_id "$outfile.id"
#end if
#if str( $__new_file_path__ ) != '' and str( $__new_file_path__ ) != 'None' :
	-o_dir "$__new_file_path__"
#end if
#if str( $max_sol ) != ''  and str( $max_sol ) != 'None' :
   -max_sol "$max_sol"
#end if
#if str( $non_opt ) != ''  and str( $non_opt ) != 'None' :
   -non_opt "$non_opt"
#end if
#if str( $scr_pen ) != ''  and str( $scr_pen ) != 'None' :
   -scr_pen "$scr_pen"
#end if
 | tail -n 1
</command>
    <inputs>
 			<param name="i" optional="false" label="input mol2-file" type="data" format="mol2"/>
			<param name="max_sol" type="integer" size="4" value="10" label="maximal number of assignment solutions"/>
			<param name="non_opt" type="boolean" checked="no" optional="true" label="compute sub-optimal assignments as well" area="true" />  
		<!--	<param name="add_hyd" type="boolean" checked="no" label="add hydrogens as well"/> -->
 			<param name="scr_pen" type="select" label="penalty score rules">
              <option value="Antechamber">Antechamber</option>
              <option value="BALL" selected="True">BALL</option>
      </param>

 		</inputs>
    <outputs>
        <data name="outfile" format="mol2"/>
    </outputs>
		<help>This tool computes optimal and suboptimal bond order assignments based on a atomic penalty function for a given ligand in mol2 file format.

Output of this tool is a number of mol2 files each containing one bond order assignment.

To upload an input file please use the upload tool (Get Data -> Upload File).

**Further information and help** can be found in our wiki http://ball-trac.bioinf.uni-sb.de/wiki/BOAConstructor.

If you use this tool, please don't forget to cite us: 

   Dehof, A.K., Rurainski, A., Bui, Q.B.A., Böcker, S., Lenhof, H.-P., Hildebrandt, A.: Automated Bond Order Assignment as an Optimization Problem. 2011. Bioinformatics. 27(5), 619-625
</help>
</tool>



