--- a/SMART/galaxy/GetFlanking.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/GetFlanking.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
 <tool id="GetFlanking" name="get flanking">
 	<description>Get the flanking regions of a set of reference.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
 	<command interpreter="python">
 		../Java/Python/GetFlanking.py -i $formatType.inputFileName1
 		#if $formatType.FormatInputFileName1 == 'bed':
@@ -55,6 +52,9 @@
 		#end if	
   		
   		-o $outputFile  
+
+		
+		
 	</command>
 
 	<inputs>
@@ -117,7 +117,7 @@
 		</conditional>
 		
 		<conditional name="OptionUpDownStream">
-			<param name="OptionUD" type="select" label="Only provide upstream/dowstream features">
+			<param name="OptionUD" type="select" label="UpStream or DownStream">
 				<option value="UpStream">UpStream</option>
 				<option value="DownStream">DownStream</option>
 				<option value="NONE" selected="true">NONE</option>
@@ -131,8 +131,8 @@
 		</conditional>
 				
 		<conditional name="OptionColinearOrAntiSens">
-			<param name="OptionCA" type="select" label="Only provide collinear/antisens features">
-				<option value="Colinear">Collinear</option>
+			<param name="OptionCA" type="select" label="Colinear or anti-sens">
+				<option value="Colinear">Colinear</option>
 				<option value="AntiSens">AntiSens</option>
 				<option value="NONE" selected="true">NONE</option>
 			</param>
@@ -172,23 +172,8 @@
 
 
   	<outputs>
-   		<data format="gff3" name="outputFile" label="[get flanking] output file"/>
+   		<data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
   	</outputs>
 	
-	<help>
-This tool prints the elements from the second set of genomic intervals which are closest to (in other words, are flanking) the elements from the first set. You can also play on different parameters:
-
-- restrict the search to downstream or upstream elements, or print downstream and upstream elements,
-
-- only consider collinear flanking elements,
-
-- only consider anti-sense flanking elements,
-
-- only consider elements which are close enough (using some given distance),
-
-- only consider flanking elements which do not overlap with the reference element.
-
-Notice that elements from the second sets may be printed at most once, whether they are the flanking element of several elements from the first or not.
-	</help>
 	
 </tool>