Mercurial > repos > iuc > bwameth

annotate bwameth.xml @ 1:404fae08ea31 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit f96ef202e742cc1d260bce023ae0d1e1499a11d8
author iuc
date Wed, 21 Dec 2016 17:49:54 -0500
parents f7094efef903
children 2e4674c16615
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
404fae08ea31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit f96ef202e742cc1d260bce023ae0d1e1499a11d8
iuc
parents: 0
diff changeset
1 <tool id="bwameth" name="bwameth" version="0.2.0.2">
0
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
2 <description>Fast and accurate aligner of BS-Seq reads.</description>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
3 <requirements>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
4 <requirement type="package" version="1.2">samtools</requirement>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
5 <requirement type="package" version="0.2.0">bwameth</requirement>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
6 </requirements>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
7 <version_command>bwameth.py --version</version_command>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
8 <command detect_errors="aggressive">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
9 <![CDATA[
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
10 #if $referenceSource.source != "indexed":
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
11 mkdir index_dir &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
12 ln -s '$referenceSource.reference' index_dir/genome.fa &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
13 bwameth.py index index_dir/genome.fa &&
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
14 #set index="index_dir/genome.fa"
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
15 #else
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
16 #set index=$referenceSource.index.fields.path
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
17 #end if
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
18
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
19 bwameth.py
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
20 -t "\${GALAXY_SLOTS:-4}"
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
21 --reference "${index}"
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
22
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
23 #if str($readGroup).strip() != "":
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
24 --read-group "${readGroup}"
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
25 #end if
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
26
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
27 #if $single_or_paired.single_or_paired_opts == 'single':
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
28 $single_or_paired.input_singles
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
29 #elif $single_or_paired.single_or_paired_opts == 'paired':
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
30 $single_or_paired.input_mate1 $single_or_paired.input_mate2
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
31 #else:
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
32 $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
33 #end if
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
34 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam -
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
35 ]]>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
36 </command>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
37 <inputs>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
38 <conditional name="referenceSource">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
39 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
40 <option value="history" selected="True">Use one from the history</option>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
41 <option value="indexed">Use a built-in index</option>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
42 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
43 <when value="history">
1
404fae08ea31 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit f96ef202e742cc1d260bce023ae0d1e1499a11d8
iuc
parents: 0
diff changeset
44 <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" />
0
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
45 </when>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
46 <when value="indexed">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
47 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
48 <options from_data_table="bwameth_indexes">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
49 <filter type="sort_by" column="2"/>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
50 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
51 </options>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
52 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
53 </when>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
54 </conditional>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
55
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
56 <conditional name="single_or_paired">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
57 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
58 <option value="single">Single-end</option>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
59 <option value="paired">Paired-end</option>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
60 <option value="paired_collection">Paired-end Dataset Collection</option>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
61 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
62 <when value="single">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
63 <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
64 </when>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
65 <when value="paired">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
66 <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
67 <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
68 </when>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
69 <when value="paired_collection">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
70 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
71 </when>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
72 </conditional>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
73 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
74 <sanitizer sanitize="False"/>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
75 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
76 </inputs>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
77 <outputs>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
78 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
79 </outputs>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
80 <tests>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
81 <test>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
82 <param name="referenceSource" value="history" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
83 <param name="reference" value="ref.fa.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
84 <param name="single_or_paired_opts" value="paired" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
85 <param name="input_mate1" value="t_R1.fastq.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
86 <param name="input_mate2" value="t_R2.fastq.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
87 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
88 </test>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
89 <test>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
90 <param name="referenceSource" value="history" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
91 <param name="reference" value="ref.fa.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
92 <param name="single_or_paired_opts" value="paired_collection" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
93 <param name="input_mate1">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
94 <collection type="paired">
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
95 <element name="forward" value="t_R1.fastq.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
96 <element name="reverse" value="t_R2.fastq.gz" />
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
97 </collection>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
98 </param>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
99 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
100 </test>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
101 </tests>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
102 <help>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
103 <![CDATA[
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
104
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
105 **What it does**
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
106
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
107 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.
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
108 ]]>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
109 </help>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
110 <citations>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
111 <citation type="bibtex">@misc{1401.1129,
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
112 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
113 Title = {Fast and accurate alignment of long bisulfite-seq reads},
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
114 Year = {2014},
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
115 Eprint = {arXiv:1401.1129},
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
116 }</citation>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
117 </citations>
f7094efef903 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
iuc
parents:
diff changeset
118 </tool>