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Updating tools/bwameth from version 0.2.6 to 0.2.7 #5262

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merged 5 commits into from
Jun 2, 2024
Merged

Updating tools/bwameth from version 0.2.6 to 0.2.7 #5262

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4055eb8
Updating tools/bwameth from version 0.2.6 to 0.2.7
Apr 20, 2023
184f402
optimize samtools
bgruening May 19, 2024
8fdffb2
Update bwameth.xml
bgruening May 19, 2024
e81beca
Update bwameth.xml
bgruening May 21, 2024
3ac7c8d
Update bwameth.xml
bgruening May 21, 2024
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7 changes: 4 additions & 3 deletions tools/bwameth/bwameth.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -78,7 +78,8 @@ bwameth.py
#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 -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o output.bam
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Please undo this change and maybe add the explanation from here

tools-iuc/tools/hisat2/hisat2.xml

Line 341 in 3e7bf5a

## Convert SAM output to sorted BAM

Maybe use exactly the command line from over there:

| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam


]]></command>
<inputs>
<conditional name="referenceSource">
Expand Down Expand Up @@ -153,7 +154,7 @@ bwameth.py

**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,
Expand Down