# HG changeset patch
# User iuc
# Date 1625903083 0
# Node ID 8681e741a037c8f3e58312726b8db71d62b1e465
# Parent  c9105910063f47d11eeebc498b8377df959aa608
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"

diff -r c9105910063f -r 8681e741a037 bowtie2_macros.xml
--- a/bowtie2_macros.xml	Tue Jan 12 16:57:59 2021 +0000
+++ b/bowtie2_macros.xml	Sat Jul 10 07:44:43 2021 +0000
@@ -24,7 +24,7 @@
         #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
diff -r c9105910063f -r 8681e741a037 bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Tue Jan 12 16:57:59 2021 +0000
+++ b/bowtie2_wrapper.xml	Sat Jul 10 07:44:43 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01">
+<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
@@ -305,9 +305,9 @@
 
 ## output file
 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
-    | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
+    | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
 #else if $sam_options.reorder:
-    | samtools view -bS - -o '$output'
+    | samtools view --no-PG -bS - -o '$output'
 #else:
     > '$output'
 #end if
diff -r c9105910063f -r 8681e741a037 test-data/bowtie2-test1.bam
Binary file test-data/bowtie2-test1.bam has changed
diff -r c9105910063f -r 8681e741a037 test-data/bowtie2-test2.bam
Binary file test-data/bowtie2-test2.bam has changed
diff -r c9105910063f -r 8681e741a037 test-data/bowtie2-test_fasta_in.bam
Binary file test-data/bowtie2-test_fasta_in.bam has changed
diff -r c9105910063f -r 8681e741a037 test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam
Binary file test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam has changed
diff -r c9105910063f -r 8681e741a037 test-data/bowtie2-test_il.bam
Binary file test-data/bowtie2-test_il.bam has changed