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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
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9:d82648ad25a3 10:cf1322aeb137
1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05"> 1 <tool id="bwameth" name="bwameth" version="@TOOL_VERSION@+galaxy0" profile="20.05">
2 <description>Fast and accurate aligner of BS-Seq reads.</description> 2 <description>Fast and accurate aligner of BS-Seq reads.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.2.6</token> 4 <token name="@TOOL_VERSION@">0.2.7</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
8 </requirements> 8 </requirements>
9 <version_command>bwameth.py --version</version_command> 9 <version_command>bwameth.py --version</version_command>
76 #if $single_or_paired.single_or_paired_opts == 'single': 76 #if $single_or_paired.single_or_paired_opts == 'single':
77 $read1 77 $read1
78 #else: 78 #else:
79 $read1 $read2 79 $read1 $read2
80 #end if 80 #end if
81 | samtools view --no-PG -u - | samtools sort --no-PG -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -o output.bam - 81 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam
82
82 ]]></command> 83 ]]></command>
83 <inputs> 84 <inputs>
84 <conditional name="referenceSource"> 85 <conditional name="referenceSource">
85 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> 86 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
86 <option value="history" selected="True">Use one from the history</option> 87 <option value="history" selected="True">Use one from the history</option>
151 </tests> 152 </tests>
152 <help><![CDATA[ 153 <help><![CDATA[
153 154
154 **What it does** 155 **What it does**
155 156
156 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. 157 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.
157 ]]></help> 158 ]]></help>
158 <citations> 159 <citations>
159 <citation type="bibtex">@misc{1401.1129, 160 <citation type="bibtex">@misc{1401.1129,
160 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, 161 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
161 Title = {Fast and accurate alignment of long bisulfite-seq reads}, 162 Title = {Fast and accurate alignment of long bisulfite-seq reads},