# HG changeset patch
# User deepakjadmin
# Date 1452091449 18000
# Node ID 1ed1be5611bbc19e28b3f048ef9c1d96423d72df
# Parent  28319c6588ffae566c44e0b9d3eb71afd9c233fd
Deleted selected files

diff -r 28319c6588ff -r 1ed1be5611bb padelnew.xml
--- a/padelnew.xml	Wed Jan 06 09:36:36 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<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>