Mercurial > repos > iuc > minimap2

changeset 17:c0c2d0941de8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b5d3813c1e592400682b7c68ebb8c240f8e86bb4"
author iuc
date Fri, 19 Nov 2021 14:35:04 +0000
parents 6b1e195506a3
children 11a0d50a54e6
files macros.xml minimap2.xml
diffstat 2 files changed, 6 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>                                                                                  
--- 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"/>