# HG changeset patch
# User deepakjadmin
# Date 1483085528 18000
# Node ID 24364e0f3b2ca2552863113022d143752d34f40e
# Parent  e22b7430ba3a782448fdcbb8870b459f2b8f8aaa
Uploaded

diff -r e22b7430ba3a -r 24364e0f3b2c padelnew.xml
--- a/padelnew.xml	Sat Dec 24 11:40:35 2016 -0500
+++ b/padelnew.xml	Fri Dec 30 03:12:08 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 $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d  $fingerprint $retainorder -file $descriptor -log > $log ;
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi $coordinate2d -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread-$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 $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d  $fingerprint $retainorder -file $descriptor -log >$log
+/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d  -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d  $fingerprint $retainorder -file $descriptor -log >$log
 #end if
 </command>
 
@@ -34,15 +34,32 @@
         	<option value = "-standardizenitro" selected="TRUE" >YES</option>
           	<option value = "" >NO</option>
 	</param>
+     
+     <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="in miliseconds" >
+        	<validator type="empty_field" message="This field can't be left blank"/>
+	</param>
+       
+       <param name="thread" type="integer" value="8" label="Workers for the job" help="set number of threads -1 for maximun " >
+        	<validator type="empty_field" message="This field can't be left blank"/>
+	</param>
+       
+       
+       <param name="maxjob" type="integer" value="-1" label="Maximum waiting job per thread. " help="put -1 for maximum uitility or put positive inetger values upto 50" >
+        	<validator type="empty_field" message="This field can't be left blank"/>
+	</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>