# HG changeset patch
# User iuc
# Date 1660935071 0
# Node ID 47c6967dc4e0c6b08f309ba2ecd510070d92f737
# Parent  22b497739c9cc075ca766feae1a51e456177da5d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0

diff -r 22b497739c9c -r 47c6967dc4e0 bwa.xml
--- a/bwa.xml	Tue Aug 31 07:48:28 2021 +0000
+++ b/bwa.xml	Fri Aug 19 18:51:11 2022 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="@VERSION@.4">
+<tool id="bwa" name="Map with BWA" version="@VERSION@.5">
     <description>- map short reads (&lt; 100 bp) against reference genome</description>
     <xrefs>
         <xref type="bio.tools">bwa</xref>
@@ -129,6 +129,7 @@
         -o ${$input_type.adv_pe_options.o}
         -n ${$input_type.adv_pe_options.n}
         -N ${$input_type.adv_pe_options.N}
+        -c ${$input_type.adv_pe_options.c}
     #end if
     @read_group_options@
     #if str( $input_type.input_type_selector ) == "paired_collection":
diff -r 22b497739c9c -r 47c6967dc4e0 read_group_macros.xml
--- a/read_group_macros.xml	Tue Aug 31 07:48:28 2021 +0000
+++ b/read_group_macros.xml	Fri Aug 19 18:51:11 2022 +0000
@@ -23,7 +23,7 @@
         #import itertools
         #set $input_name1 = $clean($identifier_or_name($input1))
         #set $input_name2 = $clean($identifier_or_name($input2))
-        #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
+        #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))])
         #if len($common_prefix) > 3
             #return $common_prefix
         #else