Mercurial > repos > devteam > bowtie2

diff bowtie2_wrapper.xml @ 27:a6d65b0c67af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
author iuc
date Sat, 10 Jul 2021 07:45:14 +0000
parents 09b2cdb7ace5
children cd659e8cc5fa
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--- a/bowtie2_wrapper.xml	Tue Jan 12 16:58:26 2021 +0000
+++ b/bowtie2_wrapper.xml	Sat Jul 10 07:45:14 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