--- a/SMART/galaxy/restrictFromSize.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/restrictFromSize.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,13 +1,8 @@
 <tool id="restrictFromSize" name="restrict from size">
 	<description>Select the elements of a list of sequences or transcripts with a given size.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
 	<command interpreter="python">
 		../Java/Python/restrictFromSize.py -i $formatType.inputFileName
-		#if $formatType.FormatInputFileName == 'fasta':
-			-f fasta
-		#elif $formatType.FormatInputFileName == 'bed':
+		#if $formatType.FormatInputFileName == 'bed':
 			-f bed
 		#elif $formatType.FormatInputFileName == 'gff':
 			-f gff
@@ -34,7 +29,6 @@
 	<inputs>
 		<conditional name="formatType">
 			<param name="FormatInputFileName" type="select" label="Input File Format">
-				<option value="fasta">fasta</option>
 				<option value="bed">bed</option>
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
@@ -42,9 +36,6 @@
 				<option value="sam">sam</option>
 				<option value="gtf">gtf</option>
 			</param>
-			<when value="fasta">
-				<param name="inputFileName" format="fasta" type="data" label="Input File"/>
-			</when>
 			<when value="bed">
 				<param name="inputFileName" format="bed" type="data" label="Input File"/>
 			</when>
@@ -92,11 +83,11 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFileGff" format="gff3" label="[restrict from size] output file"/>
+		<data name="outputFileGff" format="gff3" label="[restrictFromSize] Output File"/>
 	</outputs> 
 	
 	<help>
-Reads a list of sequences or genomic coordinates and outputs those which are longer and / or shorter than a given size ---which you provide.
+		command example: restrictFromSize.py -i cis_e10_cluster20InSeed2515_nbEUp10.gff3 -f gff -o cis_e10_cluster20InSeed2515_nbEUp10_lgUp50 -m 50
 	</help>
 
 </tool>