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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="dunovo" name="Du Novo: Make consensus reads" version="0.7">
3 <description>from duplex sequencing alignments</description>
4 <requirements>
5 <requirement type="package" version="0.7">dunovo</requirement>
6 <!-- TODO: require Python 2.7 -->
7 </requirements>
8 <command detect_errors="exit_code">dunovo.sh -r $min_reads -q $qual_thres -F $qual_format '$input' '$dcs1' '$dcs2'
9 #if $keep_sscs:
10 '$sscs1' '$sscs2'
11 #end if
12 </command>
13 <inputs>
14 <param name="input" type="data" format="tabular" label="Aligned input reads" />
15 <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
16 <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
17 <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
18 <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
19 <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
20 </param>
21 <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" />
22 </inputs>
23 <outputs>
24 <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
25 <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
26 <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)">
27 <filter>keep_sscs</filter>
28 </data>
29 <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)">
30 <filter>keep_sscs</filter>
31 </data>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input" value="families.msa.tsv"/>
36 <output name="dcs1" file="families.cons_1.fa"/>
37 <output name="dcs2" file="families.cons_2.fa"/>
38 </test>
39 </tests>
40 <citations>
41 <citation type="bibtex">@article{Stoler2016,
42 author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
43 doi = {10.1186/s13059-016-1039-4},
44 issn = {1474-760X},
45 journal = {Genome biology},
46 number = {1},
47 pages = {180},
48 pmid = {27566673},
49 publisher = {Genome Biology},
50 title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
51 url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
52 volume = {17},
53 year = {2016}
54 }</citation>
55 </citations>
56 <help>
57
58 **What it does**
59
60 This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
61
62 -----
63
64 **Input**
65
66 This expects the output format of the "Align families" tool.
67
68 -----
69
70 **Output**
71
72 This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
73
74 </help>
75 </tool>