Mercurial > repos > nick > dunovo

annotate align_families.xml @ 2:a9cb6fb9ea94 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Du Novo 0.7.6.
author nick
date Thu, 24 Aug 2017 02:13:33 -0400
parents ea832c221ec9
children 00dde366870a
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"?>
2
a9cb6fb9ea94 Update to Du Novo 0.7.6.
nick
parents: 1
diff changeset
2 <tool id="align_families" name="Du Novo: Align families" version="0.7.6">
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>
2
a9cb6fb9ea94 Update to Du Novo 0.7.6.
nick
parents: 1
diff changeset
6 <requirement type="package" version="0.7.6">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>
2
a9cb6fb9ea94 Update to Du Novo 0.7.6.
nick
parents: 1
diff changeset
9 <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$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"/>
2
a9cb6fb9ea94 Update to Du Novo 0.7.6.
nick
parents: 1
diff changeset
13 <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send anonymous 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 time taken to process it, and the IP address of the machine running it. No parameters or filenames are sent."/>
0
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
14 </inputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
15 <outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
16 <data name="output" format="tabular"/>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
17 </outputs>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
18 <tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
19 <test>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
20 <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
21 <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
22 </test>
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="families.in.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="families.sort.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 </tests>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
28 <citations>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
29 <citation type="bibtex">@article{Stoler2016,
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
30 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
31 doi = {10.1186/s13059-016-1039-4},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
32 issn = {1474-760X},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
33 journal = {Genome biology},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
34 number = {1},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
35 pages = {180},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
36 pmid = {27566673},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
37 publisher = {Genome Biology},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
38 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
39 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
40 volume = {17},
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
41 year = {2016}
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
42 }</citation>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
43 </citations>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
44 <help>
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 **What it does**
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 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
49
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
50 -----
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 **Input**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
53
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
54 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
55
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
56 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
57
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
58 **Output**
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 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
61
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
62 The columns are::
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
63
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
64 1: barcode (both tags)
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
65 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
66 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
67 4: read name
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
68 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
69 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
70
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
71 -----
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
72
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
73 **Alignments**
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
74
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
75 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
76 ::
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
77
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
78 $ 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
79
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
80 </help>
f875256c722e planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff changeset
81 </tool>