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changeset 25:e188dc7a68e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
author iuc
date Fri, 19 Aug 2022 18:51:56 +0000
parents 64f11cf59c6e
children 2477830927ec
files bwa-mem.xml bwa.xml read_group_macros.xml
diffstat 3 files changed, 9 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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":
--- 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