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<tool id="PaDEL789xsf1" name="PaDEL">
<description>"PaDEL Descriptor Calculation Tool"</description>
<command interpreter="java -jar">PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $3d  $fingerprint $retainorder -file $output1 -log >$log  </command>

<inputs>
	<param format="txt" name="input" type="data" label="sdf file"/>
  		
	<param name="detectaromaticity" type="select" label="Detect the aroamaticity">
        	<option value = "-detectaromaticity" selected="TRUE" >YES</option>
		<option value = "" >NO</option>
	</param>

	<param name="removesalt" type="select" label="Remove salt">
        	<option value = "-removesalt" selected="TRUE" >YES</option>
		<option value = "" >NO</option>
	</param>
       
        <param name="standardizenitro" type="select" label="Standardize nitro groups">
        	<option value = "-standardizenitro" selected="TRUE" >YES</option>
          	<option value = "" >NO</option>
	</param>
       
        <param name="convert3d" type="select" label="convert in 3D">
        	<option value = "" selected="TRUE" >NO</option>
        	<option value = "-convert3d" >YES</option>
  	</param>

        <param name="retain3d" type="select" label="Retain 3D coordinates">
        	<option value = "" selected="TRUE" >NO</option>
        	<option value = "-retain3d" >YES</option>
         	
	</param>
	
	<param name="3d" type="select" label="calculate 3d descriptors">
		<option value = "" selected="TRUE" >NO</option>
		<option value = "-3d" >YES</option>
	</param>

	<param name="fingerprint" type="select"  label="calculate fingerprints">
        	<option value = "" selected="TRUE" >NO</option>
        	<option value = "-fingerprints">YES</option>
	</param>

	
	<param name="retainorder" type="select" label="Retain molecules order">
        	<option value = "-retainorder" selected="TRUE">YES</option>
         	<option value = "" >NO</option>
	</param>

	
	
                  <!--
<param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
<param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" />
-->
	</inputs>

<outputs>
	<data format="txt" name="output1" label="Descriptors File"/>
	<data format="txt" name="log" label="Log File"/>
</outputs>

<help>
run command with sdf file format only and output file will be in CSV format.
</help>

</tool>