--- a/minimap2.xml	Fri Oct 08 14:43:18 2021 +0000
+++ b/minimap2.xml	Fri Nov 19 14:35:04 2021 +0000
@@ -47,6 +47,7 @@
     #if str($mapping_options.min_occ_floor):
         --min-occ-floor $mapping_options.min_occ_floor
     #end if
+    --q-occ-frac $mapping_options.q_occ_frac
     #if str($mapping_options.g):
         -g $mapping_options.g
     #end if
@@ -259,7 +260,10 @@
                 <when value="">
                 </when>
             </conditional>
-            <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
+            <param argument="--min-occ-floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
+            <param argument="--q-occ-frac" type="float" value="0.01" label="Discard a query minimizer"
+                help="Discard a query minimizer if its occurrence is higher than this fraction of query minimizers and than the reference occurrence threshold. It allows to avoid extremely long mapping time for pathologic reads with highly repeated k-mers not in the reference. Set to 0 to disable the new heuristic." />
+
             <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/>
             <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" />
             <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/>