# HG changeset patch
# User iuc
# Date 1690401733 0
# Node ID bfaa0d22c2e458e550bfc7df0937b9a68bf46164
# Parent  b4a22d90cce942159a0c98c3c27f0b9579201889
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 689a4aeaf70a8e77be8589b1dcceb190f9df626a

diff -r b4a22d90cce9 -r bfaa0d22c2e4 bwa-mem2.xml
--- a/bwa-mem2.xml	Wed Nov 24 21:29:45 2021 +0000
+++ b/bwa-mem2.xml	Wed Jul 26 20:02:13 2023 +0000
@@ -71,6 +71,9 @@
         ${analysis_type.io_options.M}
         ${analysis_type.io_options.five}
         ${analysis_type.io_options.q}
+        #if str( $analysis_type.io_options.K ):
+            -K '${analysis_type.io_options.K}'
+        #end if
     #end if
 
 #end if
@@ -238,7 +241,7 @@
                 </conditional>
 
                 <conditional name="io_options">
-                    <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
+                    <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, -M, and -K options.">
                         <option value="set">Set</option>
                         <option value="do_not_set" selected="True">Do not set</option>
                     </param>
@@ -252,6 +255,7 @@
                         <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
                         <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
                         <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
+                        <param name="K" type="integer" optional="True" label="Process this number of input bases in each batch regardless of nThreads (for reproducibility)" help="-K"/>
                     </when>
                     <when value="do_not_set">
                         <!-- do nothing -->
diff -r b4a22d90cce9 -r bfaa0d22c2e4 macros.xml
--- a/macros.xml	Wed Nov 24 21:29:45 2021 +0000
+++ b/macros.xml	Wed Jul 26 20:02:13 2023 +0000
@@ -2,7 +2,7 @@
     <import>read_group_macros.xml</import>
 
     <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
 
     <xml name="xrefs">
         <xrefs>