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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db
author iuc
date Wed, 14 Sep 2016 16:55:47 -0400
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children 404fae08ea31
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-1:000000000000 0:f7094efef903
1 <tool id="bwameth" name="bwameth" version="0.2.0">
2 <description>Fast and accurate aligner of BS-Seq reads.</description>
3 <requirements>
4 <requirement type="package" version="1.2">samtools</requirement>
5 <requirement type="package" version="0.2.0">bwameth</requirement>
6 </requirements>
7 <version_command>bwameth.py --version</version_command>
8 <command detect_errors="aggressive">
9 <![CDATA[
10 #if $referenceSource.source != "indexed":
11 mkdir index_dir &&
12 ln -s '$referenceSource.reference' index_dir/genome.fa &&
13 bwameth.py index index_dir/genome.fa &&
14 #set index="index_dir/genome.fa"
15 #else
16 #set index=$referenceSource.index.fields.path
17 #end if
18
19 bwameth.py
20 -t "\${GALAXY_SLOTS:-4}"
21 --reference "${index}"
22
23 #if str($readGroup).strip() != "":
24 --read-group "${readGroup}"
25 #end if
26
27 #if $single_or_paired.single_or_paired_opts == 'single':
28 $single_or_paired.input_singles
29 #elif $single_or_paired.single_or_paired_opts == 'paired':
30 $single_or_paired.input_mate1 $single_or_paired.input_mate2
31 #else:
32 $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse
33 #end if
34 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam -
35 ]]>
36 </command>
37 <inputs>
38 <conditional name="referenceSource">
39 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?">
40 <option value="history" selected="True">Use one from the history</option>
41 <option value="indexed">Use a built-in index</option>
42 </param>
43 <when value="history">
44 <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" />
45 </when>
46 <when value="indexed">
47 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
48 <options from_data_table="bwameth_indexes">
49 <filter type="sort_by" column="2"/>
50 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
51 </options>
52 </param>
53 </when>
54 </conditional>
55
56 <conditional name="single_or_paired">
57 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
58 <option value="single">Single-end</option>
59 <option value="paired">Paired-end</option>
60 <option value="paired_collection">Paired-end Dataset Collection</option>
61 </param>
62 <when value="single">
63 <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." />
64 </when>
65 <when value="paired">
66 <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." />
67 <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." />
68 </when>
69 <when value="paired_collection">
70 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
71 </when>
72 </conditional>
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'">
74 <sanitizer sanitize="False"/>
75 </param>
76 </inputs>
77 <outputs>
78 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" />
79 </outputs>
80 <tests>
81 <test>
82 <param name="referenceSource" value="history" />
83 <param name="reference" value="ref.fa.gz" />
84 <param name="single_or_paired_opts" value="paired" />
85 <param name="input_mate1" value="t_R1.fastq.gz" />
86 <param name="input_mate2" value="t_R2.fastq.gz" />
87 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
88 </test>
89 <test>
90 <param name="referenceSource" value="history" />
91 <param name="reference" value="ref.fa.gz" />
92 <param name="single_or_paired_opts" value="paired_collection" />
93 <param name="input_mate1">
94 <collection type="paired">
95 <element name="forward" value="t_R1.fastq.gz" />
96 <element name="reverse" value="t_R2.fastq.gz" />
97 </collection>
98 </param>
99 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
100 </test>
101 </tests>
102 <help>
103 <![CDATA[
104
105 **What it does**
106
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.
108 ]]>
109 </help>
110 <citations>
111 <citation type="bibtex">@misc{1401.1129,
112 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
113 Title = {Fast and accurate alignment of long bisulfite-seq reads},
114 Year = {2014},
115 Eprint = {arXiv:1401.1129},
116 }</citation>
117 </citations>
118 </tool>