# HG changeset patch
# User iuc
# Date 1637332467 0
# Node ID 068470a24bb554aa7f1bf85955a2e4ab6ee88fad
# Parent  39aeafbc5089361bff3e8c75f69412958dd207ad
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b5d3813c1e592400682b7c68ebb8c240f8e86bb4"

diff -r 39aeafbc5089 -r 068470a24bb5 macros.xml
--- a/macros.xml	Fri Oct 08 14:42:44 2021 +0000
+++ b/macros.xml	Fri Nov 19 14:34:27 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.22</token>
+    <token name="@TOOL_VERSION@">2.23</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
diff -r 39aeafbc5089 -r 068470a24bb5 minimap2.xml
--- a/minimap2.xml	Fri Oct 08 14:42:44 2021 +0000
+++ b/minimap2.xml	Fri Nov 19 14:34:27 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"/>