Mercurial > repos > nick > dunovo

annotate align_families.xml @ 4:5fbeaa41b223 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Du Novo 2.0.6.
author nick
date Wed, 25 Oct 2017 19:26:43 -0400
parents 00dde366870a
children 000969829a5d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
1 <?xml version="1.0"?>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
2 <tool id="align_families" name="Du Novo: Align families" version="2.0.6">
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
3 <description>of duplex sequencing reads</description>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
4 <requirements>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
5 <requirement type="package" version="7.221">mafft</requirement>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
6 <requirement type="package" version="2.0.6">dunovo</requirement>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
7 <!-- TODO: require Python 2.7 -->
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
8 </requirements>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
9 <command detect_errors="exit_code">align_families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
10 </command>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
11 <inputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
12 <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
13 <param name="aligner" type="select" value="mafft" label="Multiple sequence aligner" help="MAFFT is the original aligner Du Novo was published with in 2016. Kalign is much faster and has similar accuracy.">
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
14 <option value="kalign">Kalign2</option>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
15 <option value="mafft">MAFFT</option>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
16 </param>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
17 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, the alignment algorithm selected, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The names of the input and output datasets are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
18 </inputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
19 <outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
20 <data name="output" format="tabular"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
21 </outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
22 <tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
23 <test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
24 <param name="input" value="smoke.families.tsv"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
25 <output name="output" file="smoke.families.aligned.tsv"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
26 </test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
27 <test>
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
28 <param name="input" value="families.sort.tsv"/>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
29 <output name="output" file="families.msa.tsv"/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
30 </test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
31 </tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
32 <help>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
33
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
34 **What it does**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
35
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
36 This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
37
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
38 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
39
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
40 **Input**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
41
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
42 This expects the output format of the "Make families" tool.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
43
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
44 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
45
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
46 **Output**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
47
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
48 The output is a tabular file where each line corresponds to a (single) read.
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
49
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
50 The columns are::
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
51
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
52 1: barcode (both tags)
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
53 2: tag order in barcode ("ab" or "ba")
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
54 3: read mate ("1" or "2")
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
55 4: read name
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
56 5: read sequence, aligned ("-" for gaps)
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
57 6: read quality scores, aligned (" " for gaps)
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
58
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
59 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
60
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
61 **Alignments**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
62
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
63 The alignments are done using MAFFT, specifically the command
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
64 ::
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
65
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
66 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
67
4
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
68 </help>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
69 <citations>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
70 <citation type="bibtex">@article{Stoler2016,
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
71 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
72 doi = {10.1186/s13059-016-1039-4},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
73 issn = {1474-760X},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
74 journal = {Genome biology},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
75 number = {1},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
76 pages = {180},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
77 pmid = {27566673},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
78 publisher = {Genome Biology},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
79 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
80 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
81 volume = {17},
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
82 year = {2016}
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
83 }</citation>
5fbeaa41b223 Update to Du Novo 2.0.6.
nick
parents: 3
diff changeset
84 </citations>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
85 </tool>