# HG changeset patch
# User iuc
# Date 1626184589 0
# Node ID b4e6819b25ef17f3c0b1cc66e6bd6bf25b3672be
# Parent  29bdbc353f20a8433031abeaa02f64d362915a12
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 6d44811a45b4f6fded1ec72450ed300318095ce4"

diff -r 29bdbc353f20 -r b4e6819b25ef bwameth.xml
--- a/bwameth.xml	Tue Oct 01 17:53:32 2019 -0400
+++ b/bwameth.xml	Tue Jul 13 13:56:29 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01">
+<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy1" profile="20.05">
     <description>Fast and accurate aligner of BS-Seq reads.</description>
     <macros>
         <token name="@TOOL_VERSION@">0.2.2</token>
@@ -78,7 +78,7 @@
 #else:
     $read1 $read2
 #end if
-| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
+| samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
     ]]></command>
     <inputs>
         <conditional name="referenceSource">
@@ -130,7 +130,7 @@
             <param name="single_or_paired_opts" value="paired" />
             <param name="input_mate1" value="t_R1.fastq.gz"/>
             <param name="input_mate2" value="t_R2.fastq.gz"/>
-            <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
+            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
         </test>
         <test>
             <param name="referenceSource" value="history" />
@@ -142,7 +142,7 @@
                     <element name="reverse" value="t_R2.fastq.gz"/>
                 </collection>
             </param>
-            <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
+            <output file="output.bam" ftype="bam" name="output" lines_diff="4"/><!-- allow for HD and PG lines diff-->
         </test>
     </tests>
     <help><![CDATA[