# HG changeset patch
# User iuc
# Date 1717346303 0
# Node ID cf1322aeb137f06d8157dec0e3ba56da9892c1e8
# Parent  d82648ad25a31206e255d2b8a8fdfe9023c046ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 16f1bd9f85b90ad12dbb43bc00ebe469620cfd04

diff -r d82648ad25a3 -r cf1322aeb137 bwameth.xml
--- a/bwameth.xml	Mon Mar 20 20:39:36 2023 +0000
+++ b/bwameth.xml	Sun Jun 02 16:38:23 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05">
     <description>Fast and accurate aligner of BS-Seq reads.</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.2.6</token>
+        <token name="@TOOL_VERSION@">0.2.7</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
@@ -78,7 +78,8 @@
 #else:
     $read1 $read2
 #end if
-| samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam -
+| samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1}  -o output.bam
+
     ]]></command>
     <inputs>
         <conditional name="referenceSource">
@@ -153,7 +154,7 @@
 
 **What it does**
 
-BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
+BWA-meth performs the alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. This methodology is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
     ]]></help>
     <citations>
         <citation type="bibtex">@misc{1401.1129,