--- a/csem.xml	Mon Sep 12 10:15:59 2011 -0400
+++ b/csem.xml	Mon Sep 12 10:31:48 2011 -0400
@@ -50,11 +50,11 @@
 			<validator type="no_options" message="No indexes are available" />
 		</options>
 	</param>
-	<param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats.">
-		<option value="fasta">FASTA</option>
-		<option value="fastq">FASTQ</option>
-	</param>
-	<conditional name="InfileFormat">
+	<conditional name="InputParams">
+		<param name="InfileFormat" type="select" label="Select file format to process" help="Bowtie accepts FASTA or FASTQ file formats.">
+			<option value="fasta">FASTA</option>
+			<option value="fastq">FASTQ</option>
+		</param>
 		<when value="fasta">
 			<param name="Input" type="data" format="fasta" label="FASTA file"/>
 		</when>
@@ -70,23 +70,23 @@
 	<param name="pseudoTag" type="select" label="Generate pseudo-tags?" help="See section 'Pseudo-tags' in the help below for more details.">
 		<option value="N">NO</option>
 		<option value="Y">YES</option>
-	</param>
-	<param name="bSettingsType" type="select" label="Bowtie settings to use" help="For most mapping applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'.">
-		<option value="preSet">Commonly used</option>
-		<option value="full">Full parameter list</option>
 	</param>		
-	<conditional name="bSettingsType">
+	<conditional name="bowtieParams">
+		<param name="bSettingsType" type="select" label="Bowtie settings to use" help="For most mapping applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'.">
+			<option value="preSet">Commonly used</option>
+			<option value="full">Full parameter list</option>
+		</param>
 		<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." />
 			<param name="SuppressAlign" type="integer" value="99" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="99 is appropriate for most cases. Use -1 for no limit." />
 		</when> <!-- full -->
-	</conditional> <!-- bowtieParams -->
-	<param name="cSettingsType" type="select" label="CSEM settings to use" help="For most multi-read allocation applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'.">
-		<option value="preSet">Commonly used</option>
-		<option value="full">Full parameter list</option>
-	</param>		
-	<conditional name="cSettingsType">
+	</conditional> <!-- bowtieParams -->		
+	<conditional name="csemParams">
+		<param name="cSettingsType" type="select" label="CSEM settings to use" help="For most multi-read allocation applications, use the 'Commonly used' settings. If you want full control, use 'Full parameter list'.">
+			<option value="preSet">Commonly used</option>
+			<option value="full">Full parameter list</option>
+		</param>
 		<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." />