--- a/SMART/galaxy/SelectByTag.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/SelectByTag.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,16 +1,17 @@
 <tool id="SelectByTag" name="select by tag">
-	<description>Keep the genomic coordinates such that a value of a given tag.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
+	<description>Keeps 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
@@ -36,11 +37,16 @@
 	<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>
@@ -50,6 +56,9 @@
 			<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>
@@ -58,12 +67,12 @@
 		<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="given value for the tag">
+			<param name="Value" type="select" label="value of tag">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="valeur" type="integer" value="1"/>
+				<param name="valeur" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
 			</when>
 			<when value="No">
 			</when>
@@ -75,7 +84,7 @@
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="max" type="integer" value="1"/>
+				<param name="max" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
 			</when>
 			<when value="No">
 			</when>
@@ -87,14 +96,14 @@
 				<option value="No" selected="true">No</option>
 			</param>
 			<when value="Yes">
-				<param name="min" type="integer" value="1"/>
+				<param name="min" type="integer" value="1" help="Be Careful! The value must be upper than 0"/>
 			</when>
 			<when value="No">
 			</when>
 		</conditional>	
 		
 		<conditional name="OptionDefault">
-			<param name="default" type="select" label="give this value if tag is not present">
+			<param name="default" type="select" label="gives this value if tag is not present">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -107,16 +116,7 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFileGff" format="gff3" label="[select by tag] output file"/>
+		<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>