Mercurial > repos > iuc > bwameth
changeset 10:cf1322aeb137 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 16f1bd9f85b90ad12dbb43bc00ebe469620cfd04
| author | iuc |
|---|---|
| date | Sun, 02 Jun 2024 16:38:23 +0000 |
| parents | d82648ad25a3 |
| children | |
| files | bwameth.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- 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,