--- a/query.xml	Thu Apr 05 06:22:42 2018 -0400
+++ b/query.xml	Fri Apr 13 07:51:29 2018 -0400
@@ -12,6 +12,7 @@
     --tree 1
     --search 'rrr'
     --sthreshold ${sthreshold}
+    --sort ${sortcontrol}
     --exact 0
     
     #if $conditional_input.inputtype == '0':
@@ -42,6 +43,7 @@
             </when>
         </conditional>            
         <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
+        <param name="sortcontrol" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort the result by the number of hits per transcript." />
     </inputs>
     <outputs>
         <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection">