--- a/define_clones.xml	Mon Aug 15 10:06:24 2016 -0400
+++ b/define_clones.xml	Thu Sep 15 03:54:33 2016 -0400
@@ -11,7 +11,7 @@
 		<param name="input" type="data" format="tabular" label="A Change-O DB file" />
 		<conditional name="input_type">
 			<param name="input_type_select" type="select" label="Input type">
-				<option value="bygroup">Define clones by V assignment, J assignment and junction length</option>
+				<option value="bygroup" selected="true">Define clones by V assignment, J assignment and junction length</option>
 				<option value="hclust">Define clones by specified distance metric on CDR3s and cutting of hierarchical clustering tree</option>
 			</param>
 			<when value="bygroup">
@@ -20,29 +20,29 @@
 					<option value="gene" selected="true">Gene</option>
 				</param>
 				<param name="act" type="select" label="Specifies how to handle multiple V(D)J assignments for initial grouping.">
-					<option value="first">First</option>
-					<option value="set" selected="true">Set</option>
+					<option value="first" selected="true">First</option>
+					<option value="set">Set</option>
 				</param>
 				<param name="model" type="select" label="Specifies which substitution model to use for calculating distance between sequences.">
 					<option value="aa">AA hamming distance</option>
-					<option value="ham">Nucleotide hamming distance</option>
+					<option value="ham" selected="true">Nucleotide hamming distance</option>
 					<option value="m1n">Mouse single nucleotide (Smith et al, 1996)</option>
-					<option value="hs1f" selected="true">Human single nucleotide (Yaari et al, 2013)</option>
+					<option value="hs1f">Human single nucleotide (Yaari et al, 2013)</option>
 					<option value="hs5f">Human S5F (Yaari et al, 2013)</option>
 				</param>
 				<param name="norm" type="select" label="Specifies how to normalize distances.">
-					<option value="none">Do not normalize</option>
+					<option value="none" selected="true">Do not normalize</option>
 					<option value="mut">Normalize by number of mutations</option>
-					<option value="len" selected="true">Normalize by length</option>
+					<option value="len">Normalize by length</option>
 				</param>
 				<param name="sym" type="select" label="Specifies how to combine asymmetric distances.">
-					<option value="avg" selected="true">Average</option>
-					<option value="min">Minimum</option>
+					<option value="avg">Average</option>
+					<option value="min" selected="true">Minimum</option>
 				</param>
 				<param name="link" type="select" label="Type of linkage to use for hierarchical clustering.">
-					<option value="single" selected="true">Single</option>
+					<option value="single">Single</option>
 					<option value="average">Average</option>
-					<option value="complete">Complete</option>
+					<option value="complete" selected="true">Complete</option>
 				</param>
 				<param name="dist" size="4" type="float" value="0.0" label="The distance threshold for clonal grouping" />
 			</when>