--- a/SMART/galaxy/cleanGff.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/cleanGff.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
 <tool id="cleanGff" name="clean Gff">
-	  <description>Cleans a GFF file as given by NCBI and outpus a Gff3 file.</description>
+	  <description>Clean a GFF file (e.g. as given by NCBI) and produces a new GFF3 file, understood by S-MART.</description>
 	  <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile 
 		  -t $type 
 		  -o $outputFile
@@ -7,12 +7,15 @@
 
 	      <inputs>
 		      <param name="inputFile" type="data" label="Input File" format="gff"/>
-		      <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="tag option, compulsory option" help="lists of comma separated types that you want to keep.EX: ncRNA,tRNA,rRNA,CDS"/>
+		      <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="Tags you keep" help="lists of comma separated types that you want to keep, e.g. ncRNA,tRNA,rRNA,CDS"/>
 	      </inputs>
 
 	      <outputs>
 	          <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
 	      </outputs>
 
+	<help>
+		A GFF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about it) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input GFF3 to keep the information you really want, based on the feature (3rd column).
+	</help>
 </tool>