# HG changeset patch
# User deepakjadmin
# Date 1452091484 18000
# Node ID c1ebd651da65dd59d9a866b3f0b0040ecf03a3d4
# Parent  1ed1be5611bbc19e28b3f048ef9c1d96423d72df
Uploaded

diff -r 1ed1be5611bb -r c1ebd651da65 padelnew.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/padelnew.xml	Wed Jan 06 09:44:44 2016 -0500
@@ -0,0 +1,83 @@
+<tool id="PaDEL789xsf1" name="PaDEL">
+<requirements>
+     
+    <requirement type="package" version="2.21">padel</requirement>
+   
+</requirements>
+
+
+<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 ${PACKAGE_BASE}/bin/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 ${PACKAGE_BASE}/bin/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>