# HG changeset patch
# User iuc
# Date 1637332504 0
# Node ID c0c2d0941de88060423d697718ad39fe43df73a0
# Parent  6b1e195506a3fb68a2060905d04e7c39da29b3b0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b5d3813c1e592400682b7c68ebb8c240f8e86bb4"

diff -r 6b1e195506a3 -r c0c2d0941de8 macros.xml
--- a/macros.xml	Fri Oct 08 14:43:18 2021 +0000
+++ b/macros.xml	Fri Nov 19 14:35:04 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 6b1e195506a3 -r c0c2d0941de8 minimap2.xml
--- 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"/>