Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4/mira4_bait.xml @ 15:b0ffe0e7282b draft
Uploaded v0.0.2 preview 7, fixed bash syntax error
author | peterjc |
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date | Thu, 20 Feb 2014 05:07:19 -0500 |
parents | 79759fdec6cb |
children | 381aa262c8cb |
rev | line source |
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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> | |
15 | 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" /> | |
9 | 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> | |
15 | 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" /> | |
9 | 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> | |
15 | 43 </data> |
9 | 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" /> | |
10
79759fdec6cb
Uploaded v0.0.2 preview 2, attempt auto-install for 64 bit Mac OS X.
peterjc
parents:
9
diff
changeset
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50 </test> |
9 | 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> |