--- a/csem.xml	Mon Sep 12 10:12:22 2011 -0400
+++ b/csem.xml	Mon Sep 12 10:15:59 2011 -0400
@@ -54,7 +54,7 @@
 		<option value="fasta">FASTA</option>
 		<option value="fastq">FASTQ</option>
 	</param>
-	<conditional name="InputParams">
+	<conditional name="InfileFormat">
 		<when value="fasta">
 			<param name="Input" type="data" format="fasta" label="FASTA file"/>
 		</when>
@@ -75,7 +75,7 @@
 		<option value="preSet">Commonly used</option>
 		<option value="full">Full parameter list</option>
 	</param>		
-	<conditional name="bowtieParams">
+	<conditional name="bSettingsType">
 		<when value="preSet" />
 		<when value="full">
 			<param name="Mismatch" type="integer" value="2" label="Maximum number of mismatches permitted (-v)" help="May be 0, 1, 2, or 3." />
@@ -86,7 +86,7 @@
 		<option value="preSet">Commonly used</option>
 		<option value="full">Full parameter list</option>
 	</param>		
-	<conditional name="csemParams">
+	<conditional name="cSettingsType">
 		<when value="preSet" />
 		<when value="full">
 			<param name="windowSize" type="integer" value="101" label="Window size for the multi-read allocator" help="Set window size to some odd number close to the half of average fragment length." />