# HG changeset patch
# User deepakjadmin
# Date 1482597635 18000
# Node ID e22b7430ba3a782448fdcbb8870b459f2b8f8aaa
# Parent  662b81ac6217c62a8f8f064f57db84758c0729b1
Uploaded

diff -r 662b81ac6217 -r e22b7430ba3a padelnew.xml
--- a/padelnew.xml	Thu Jan 14 05:54:37 2016 -0500
+++ b/padelnew.xml	Sat Dec 24 11:40:35 2016 -0500
@@ -10,10 +10,10 @@
 #if '.smi' in $input.name
 /bin/mkdir $input.extra_files_path;
 ln -s $input $input.extra_files_path/molecule.smi;
-/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate  $fingerprint $retainorder -file $descriptor -log > $log ;
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d  $fingerprint $retainorder -file $descriptor -log > $log ;
 /bin/rm -rf $input.extra_files_path;
 #else
-/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate  $fingerprint $retainorder -file $descriptor -log >$log
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d  $fingerprint $retainorder -file $descriptor -log >$log
 #end if
 </command>
 
@@ -46,10 +46,16 @@
          	
 	</param>
 	
-	<param name="coordinate" type="select" label="calculate 3d descriptors">
+	<param name="coordinate3d" type="select" label="calculate 3d descriptors">
 		<option value = "" selected="TRUE" >NO</option>
 		<option value = "-3d" >YES</option>
 	</param>
+	
+	<param name="coordinate2d" type="select" label="calculate 2d descriptors">
+		<option value = ""  >NO</option>
+		<option value = "-2d" selected="TRUE" >YES</option>
+	</param>
+	
 
 	<param name="fingerprint" type="select"  label="calculate fingerprints">
         	<option value = "" selected="TRUE" >NO</option>