# HG changeset patch
# User iuc
# Date 1660935116 0
# Node ID e188dc7a68e62a0ee7ce9729e75a5484282a3550
# Parent  64f11cf59c6edcb9ed9747829ef1d31e8ce1e1c5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0

diff -r 64f11cf59c6e -r e188dc7a68e6 bwa-mem.xml
--- a/bwa-mem.xml	Wed May 05 18:22:08 2021 +0000
+++ b/bwa-mem.xml	Fri Aug 19 18:51:56 2022 +0000
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
     <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
+    <xrefs>
+        <xref type="bio.tools">bwa</xref>
+    </xrefs>
     <macros>
         <import>read_group_macros.xml</import>
         <import>bwa_macros.xml</import>
diff -r 64f11cf59c6e -r e188dc7a68e6 bwa.xml
--- a/bwa.xml	Wed May 05 18:22:08 2021 +0000
+++ b/bwa.xml	Fri Aug 19 18:51:56 2022 +0000
@@ -1,6 +1,9 @@
 <?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>
+    </xrefs>
     <macros>
         <import>read_group_macros.xml</import>
         <import>bwa_macros.xml</import>
@@ -126,6 +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 64f11cf59c6e -r e188dc7a68e6 read_group_macros.xml
--- a/read_group_macros.xml	Wed May 05 18:22:08 2021 +0000
+++ b/read_group_macros.xml	Fri Aug 19 18:51:56 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