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<tool id="aaapadel001" name="PaDEL">
<description>"PaDEL Descriptor Calculation Tool"</description>
<command interpreter="">
#if '.smi' in $input.name
/bin/mkdir $input.extra_files_path;
ln -s $input $input.extra_files_path/molecule.smi;
/usr/bin/java -jar $__root_dir__/tools/PaDEL/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate  $fingerprint $retainorder -file $descriptor -log > $log ;
/bin/rm -rf $input.extra_files_path;
#else
/usr/bin/java -jar $__root_dir__/tools/PaDEL/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate  $fingerprint $retainorder -file $descriptor -log >$log
#end if
</command>

<inputs>
	<param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
  		
	<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="coordinate" 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="csv" name="descriptor" label="Descriptors File of $input.name "/>
	<data format="txt" name="log" label="Log File of $input.name"/>
</outputs>

<help>
Input may be any sdf,smile or mol2 file  and output file will be in CSV format.
</help>

</tool>