|
9
|
1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.1">
|
|
|
2 <description>Filter reads using kmer matches</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="binary">mirabait</requirement>
|
|
|
5 <requirement type="package" version="4.0">MIRA</requirement>
|
|
|
6 </requirements>
|
|
|
7 <version_command interpreter="python">mira4_bait.py --version</version_command>
|
|
|
8 <command interpreter="python">
|
|
|
9 mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads"
|
|
|
10 </command>
|
|
|
11 <stdio>
|
|
|
12 <!-- Assume anything other than zero is an error -->
|
|
|
13 <exit_code range="1:" />
|
|
|
14 <exit_code range=":-1" />
|
|
|
15 </stdio>
|
|
|
16 <inputs>
|
|
|
17 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
|
|
|
18 <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
|
|
|
19 <param name="output_choice" type="select" label="Output positive matches, or negative matches?">
|
|
|
20 <option value="pos">Just positive matches</option>
|
|
|
21 <option value="neg">Just negative matches</option>
|
|
|
22 </param>
|
|
|
23 <param name="strand_choice" type="select" label="Check for matches on both strands?">
|
|
|
24 <option value="both">Check both strands</option>
|
|
|
25 <option value="fwd">Just forward strand</option>
|
|
|
26 </param>
|
|
|
27 <param name="kmer_length" type="integer" value="31" min="1" max="32"
|
|
|
28 label="k-mer length" help="Maximum 32" />
|
|
|
29 <param name="min_occurence" type="integer" value="1" min="1"
|
|
|
30 label="Minimum k-mer occurence"
|
|
|
31 help="How many k-mer matches do you want per read? Minimum one" />
|
|
|
32 </inputs>
|
|
|
33 <outputs>
|
|
|
34 <data name="output_reads" format="fasta" label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name">
|
|
|
35 <!-- TODO - Replace this with format="input:input_reads" if/when that works -->
|
|
|
36 <change_format>
|
|
|
37 <when input_dataset="input_reads" attribute="extension" value="fastq" format="fastq" />
|
|
|
38 <when input_dataset="input_reads" attribute="extension" value="fastqsanger" format="fastqsanger" />
|
|
|
39 <when input_dataset="input_reads" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
|
|
|
40 <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" />
|
|
|
41 <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
|
|
|
42 </change_format>
|
|
|
43 </data>
|
|
|
44 </outputs>
|
|
|
45 <tests>
|
|
|
46 <test>
|
|
|
47 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
|
|
|
48 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
|
|
|
49 <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
|
|
|
50 </test>
|
|
|
51 <test>
|
|
|
52 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
|
|
|
53 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
|
|
|
54 <param name="kmer_length" value="32" />
|
|
|
55 <param name="min_occurence" value="50" />
|
|
|
56 <output name="output_reads" file="tvc_mini_bait_strict.fastq" ftype="fastqsanger" />
|
|
|
57 </test>
|
|
|
58 <test>
|
|
|
59 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
|
|
|
60 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
|
|
|
61 <param name="output_choice" value="neg" />
|
|
|
62 <output name="output_reads" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
|
|
|
63 </test>
|
|
|
64 </tests>
|
|
|
65 <help>
|
|
|
66 **What it does**
|
|
|
67
|
|
|
68 Runs the ``mirabait`` utility from MIRA v4.0 to filter your input reads
|
|
|
69 according to whether or not they contain perfect kmer matches to your
|
|
|
70 bait file. By default this looks for 31-mers (kmers or *k*-mers where
|
|
|
71 the fragment length *k* is 31), and only requires a single matching kmer.
|
|
|
72
|
|
|
73 The ``mirabait`` utility is useful in many applications and pipelines
|
|
|
74 outside of using the main MIRA tool for assembly or mapping.
|
|
|
75
|
|
|
76 .. class:: warningmark
|
|
|
77
|
|
|
78 Note ``mirabait`` cannot be used on protein (amino acid) sequences.
|
|
|
79
|
|
|
80 **Example Usage**
|
|
|
81
|
|
|
82 To remove over abundant entries like rRNA sequences, run ``mirabait`` with
|
|
|
83 known rRNA sequences as the bait and select the *negative* matches.
|
|
|
84
|
|
|
85 To do targeted assembly by fishing out reads belonging to a gene and just
|
|
|
86 assemble these, run ``mirabait`` with the gene of interest as the bait and
|
|
|
87 select the *positive* matches.
|
|
|
88
|
|
|
89 To iteratively reconstruct mitochondria you could start by fishing out reads
|
|
|
90 matching any known mitochondrial sequence, assembly those, and repeat.
|
|
|
91
|
|
|
92
|
|
|
93 **Notes on paired read**
|
|
|
94
|
|
|
95 .. class:: warningmark
|
|
|
96
|
|
|
97 While MIRA4 is aware of many read naming conventions to identify paired read
|
|
|
98 partners, the ``mirabait`` tool considers each read in isolation. Applying
|
|
|
99 it to paired read files may leave you with orphaned reads.
|
|
|
100
|
|
|
101
|
|
|
102 **Citation**
|
|
|
103
|
|
|
104 If you use this Galaxy tool in work leading to a scientific publication please
|
|
|
105 cite the following papers:
|
|
|
106
|
|
|
107 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
|
|
|
108 Galaxy tools and workflows for sequence analysis with applications
|
|
|
109 in molecular plant pathology. PeerJ 1:e167
|
|
|
110 http://dx.doi.org/10.7717/peerj.167
|
|
|
111
|
|
|
112 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
|
|
|
113 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
|
|
|
114 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
|
|
|
115 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
|
|
|
116
|
|
|
117 This wrapper is available to install into other Galaxy Instances via the Galaxy
|
|
|
118 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
|
|
|
119 </help>
|
|
|
120 </tool>
|
