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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
author nick
date Sat, 18 Feb 2017 05:58:44 -0500
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1 <?xml version="1.0"?>
2 <tool id="align_families" name="Du Novo: Align families" version="0.7">
3 <description>of duplex sequencing reads</description>
4 <requirements>
5 <requirement type="package" version="7.221">mafft</requirement>
6 <requirement type="package" version="0.7">dunovo</requirement>
7 <!-- TODO: require Python 2.7 -->
8 </requirements>
9 <command detect_errors="exit_code">align_families.py -p \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
10 </command>
11 <inputs>
12 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
13 </inputs>
14 <outputs>
15 <data name="output" format="tabular"/>
16 </outputs>
17 <tests>
18 <test>
19 <param name="input" value="smoke.families.tsv"/>
20 <output name="output" file="smoke.families.aligned.tsv"/>
21 </test>
22 <test>
23 <param name="input" value="families.in.tsv"/>
24 <output name="output" file="families.sort.tsv"/>
25 </test>
26 </tests>
27 <citations>
28 <citation type="bibtex">@article{Stoler2016,
29 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
30 doi = {10.1186/s13059-016-1039-4},
31 issn = {1474-760X},
32 journal = {Genome biology},
33 number = {1},
34 pages = {180},
35 pmid = {27566673},
36 publisher = {Genome Biology},
37 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
38 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
39 volume = {17},
40 year = {2016}
41 }</citation>
42 </citations>
43 <help>
44
45 **What it does**
46
47 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
48
49 -----
50
51 **Input**
52
53 This expects the output format of the "Make families" tool.
54
55 -----
56
57 **Output**
58
59 The output is a tabular file where each line corresponds to a (single) read.
60
61 The columns are::
62
63 1: barcode (both tags)
64 2: tag order in barcode ("ab" or "ba")
65 3: read mate ("1" or "2")
66 4: read name
67 5: read sequence, aligned ("-" for gaps)
68 6: read quality scores, aligned (" " for gaps)
69
70 -----
71
72 **Alignments**
73
74 The alignments are done using MAFFT, specifically the command
75 ::
76
77 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
78
79 </help>
80 </tool>