--- a/chira_merge.xml	Fri May 29 06:58:21 2020 -0400
+++ b/chira_merge.xml	Sat Jun 06 08:17:43 2020 -0400
@@ -12,6 +12,7 @@
         #end if
         -so '$segment_overlap'
         -lt '$length_threshold'
+        -ao '$alignment_overlap'
         #if str($merge.mode) == "blockbuster":
             -bb
             -d '$merge.distance'
@@ -19,7 +20,6 @@
             -mb '$merge.min_block_height'
             -sc '$merge.scale'
         #else:
-            -ao '$merge.alignment_overlap'
             -ls '$merge.min_locus_size'
         #end if
         #if str($reference.ref_type) == "split":
@@ -48,14 +48,14 @@
             help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
         <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
             help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
+        <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments/blocks" min="0" max="1"
+            help="Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge"/>
         <conditional name="merge">
             <param name="mode" type="select" label="Select the mode of merging">
                 <option value="overlap">Overlap based</option>
                 <option value="blockbuster">Gaussian based (blockbuster)</option>
             </param>
             <when value="overlap">
-                <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
-                    help="Minimum fraction of BED entries that must overlap inorder to merge"/>
                 <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
                             help="Minimum number of alignments to be present to output the merged a locus"/>
             </when>
@@ -140,7 +140,7 @@
             <param name="gtf" value="annotation.gtf" />
             <param name="mode" value="blockbuster" />
             <param name="min_block_height" value="1" />
-            <param name="min_cluster_height" value="5" />
+            <param name="min_cluster_height" value="0" />
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>