--- a/SMART/galaxy/SelectByTag.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/SelectByTag.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,17 +1,13 @@
 <tool id="SelectByTag" name="select by tag">
-	<description>Keeps the genomic coordinates such that a value of a given tag.</description>
+	<description>Keep the genomic coordinates such that a value of a given tag.</description>
 	<command interpreter="python">
 		../Java/Python/SelectByTag.py -i $formatType.inputFileName
-		#if $formatType.FormatInputFileName == 'bed':
-			-f bed
 		#elif $formatType.FormatInputFileName == 'gff':
 			-f gff
 		#elif $formatType.FormatInputFileName == 'gff2':
 			-f gff2
 		#elif $formatType.FormatInputFileName == 'gff3':
 			-f gff3
-		#elif $formatType.FormatInputFileName == 'sam':
-			-f sam
 		#elif $formatType.FormatInputFileName == 'gtf':
 			-f gtf
 		#end if
@@ -37,16 +33,11 @@
 	<inputs>
 		<conditional name="formatType">
 			<param name="FormatInputFileName" type="select" label="Input File Format">
-				<option value="bed">bed</option>
 				<option value="gff">gff</option>
 				<option value="gff2">gff2</option>
 				<option value="gff3">gff3</option>
-				<option value="sam">sam</option>
 				<option value="gtf">gtf</option>
 			</param>
-			<when value="bed">
-				<param name="inputFileName" format="bed" type="data" label="Input File"/>
-			</when>
 			<when value="gff">
 				<param name="inputFileName" format="gff" type="data" label="Input File"/>
 			</when>
@@ -56,9 +47,6 @@
 			<when value="gff3">
 				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
 			</when>
-			<when value="sam">
-				<param name="inputFileName" format="sam" type="data" label="Input File"/>
-			</when>
 			<when value="gtf">
 				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
 			</when>
@@ -67,12 +55,12 @@
 		<param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
 				
 		<conditional name="OptionValue">
-			<param name="Value" type="select" label="value of tag">
+			<param name="Value" type="select" label="given value for the tag">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
+				<param name="valeur" type="integer" value="1"/>
 			</when>
 			<when value="No">
 			</when>
@@ -84,7 +72,7 @@
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
+				<param name="max" type="integer" value="1"/>
 			</when>
 			<when value="No">
 			</when>
@@ -96,14 +84,14 @@
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
+				<param name="min" type="integer" value="1"/>
 			</when>
 			<when value="No">
 			</when>
 		</conditional>	
 		
 		<conditional name="OptionDefault">
-			<param name="default" type="select" label="gives this value if tag is not present">
+			<param name="default" type="select" label="give this value if tag is not present">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -119,4 +107,13 @@
 		<data name="outputFileGff" format="gff3" label="[SelectByTag] Output File"/>
 	</outputs> 
 	
+	<help>
+The script reads a list of genomic coordinates and output all the features with specific tag values. If you want to know more about tags, please consult the GFF format page: http://www.sequenceontology.org/gff3.shtml
+
+The tools reads the input file, and more specifically the tag that you specified. You can mention a lower and a upper bound for its value, or a specific value, and the tool will print all the features such that the tags are between the specified bounds or matches the string.
+
+A tag has to be present for each feature. If not, you can specify a default value which will be used if the tag is absent.
+
+This tool can be used to select the clusters with a minimum number of elements (the tag **nbElements** counts the number of elements per clusters) or to select the reads which have mapped less than *n* times (the tag **nbOccurrences** counts the number of mappings per read).
+	</help>
 </tool>