<tool id="molecularfileconverter" name="MolecularFileConverter" version="0.9.6" force_history_refresh="True"> 
		<description>converts molecular file-formats</description>
		<command>ln -s $i ${i}.${i.extension}; /usr/local/ballaxy/build/MolecularFileConverter 
#if str( $i ) != ''  and str( $i ) != 'None' :
	-i "${i}.${i.extension}"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $of ) != '' and str( $of ) != 'None' :
	-of "$of"
#end if
	| tail -n 1 ; rm ${i}.${i.extension}
</command>
    <inputs>
			<param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf/pdb/mol/hin/ac/xyz"/>
 			<param name="of" type="select" label="output format">
              <option value="mol2" selected="True">mol2</option>
              <option value="sdf">sdf</option>
              <option value="drf">drf</option>
              <option value="pdb">pdb</option>
              <option value="ac">ac</option>
              <option value="hin">hin</option>
              <option value="mol">mol</option>
              <option value="xyz">xyz</option>
      </param>
 		</inputs>
    <outputs>
			<data  format="mol2" name="o">
				<change_format>
					<when input="of" value="sdf" format="sdf" />
					<when input="of" value="drf" format="drf" />
					<when input="of" value="ac"  format="ac"  />
					<when input="of" value="hin" format="hin" />
					<when input="of" value="mol" format="mol" />
					<when input="of" value="xyz" format="xyz" />
				</change_format>
			</data>
    </outputs>
		<help>This tool converts different molecular file formats into each other.

**mol2**

Sybol Mol2 format

-----

**mol**

MDL MOL format

-----

**pdb**

Protein Data Bank format

-----

**sdf**

MDL structure data file format

-----

**hin**

HyperChem HIN format

-----

**ac**

Antechamber file format

-----

**xyz**

XYZ cartesian coordinates format
		
		</help>
</tool>



