Mercurial > repos > peterjc > mira4_assembler
annotate tools/mira4/mira4_bait.xml @ 20:aeb3e35f8236 draft
Uploaded v0.0.4 preview, made MAF and BAM output optional
| author | peterjc |
|---|---|
| date | Tue, 10 Jun 2014 10:11:58 -0400 |
| parents | 8487d70e82aa |
| children |
| rev | line source |
|---|---|
| 19 | 1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.3"> |
| 9 | 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> | |
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34 <data name="output_reads" format="input" metadata_source="input_reads" |
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Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
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35 label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/> |
| 9 | 36 </outputs> |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | |
| 40 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 41 <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" /> | |
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42 </test> |
| 9 | 43 <test> |
| 44 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | |
| 45 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 46 <param name="kmer_length" value="32" /> | |
| 47 <param name="min_occurence" value="50" /> | |
| 48 <output name="output_reads" file="tvc_mini_bait_strict.fastq" ftype="fastqsanger" /> | |
| 49 </test> | |
| 50 <test> | |
| 51 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" /> | |
| 52 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" /> | |
| 53 <param name="output_choice" value="neg" /> | |
| 54 <output name="output_reads" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" /> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help> | |
| 58 **What it does** | |
| 59 | |
| 60 Runs the ``mirabait`` utility from MIRA v4.0 to filter your input reads | |
| 61 according to whether or not they contain perfect kmer matches to your | |
| 62 bait file. By default this looks for 31-mers (kmers or *k*-mers where | |
| 63 the fragment length *k* is 31), and only requires a single matching kmer. | |
| 64 | |
| 65 The ``mirabait`` utility is useful in many applications and pipelines | |
| 66 outside of using the main MIRA tool for assembly or mapping. | |
| 67 | |
| 68 .. class:: warningmark | |
| 69 | |
| 70 Note ``mirabait`` cannot be used on protein (amino acid) sequences. | |
| 71 | |
| 72 **Example Usage** | |
| 73 | |
| 74 To remove over abundant entries like rRNA sequences, run ``mirabait`` with | |
| 75 known rRNA sequences as the bait and select the *negative* matches. | |
| 76 | |
| 77 To do targeted assembly by fishing out reads belonging to a gene and just | |
| 78 assemble these, run ``mirabait`` with the gene of interest as the bait and | |
| 79 select the *positive* matches. | |
| 80 | |
| 81 To iteratively reconstruct mitochondria you could start by fishing out reads | |
| 82 matching any known mitochondrial sequence, assembly those, and repeat. | |
| 83 | |
| 84 | |
| 85 **Notes on paired read** | |
| 86 | |
| 87 .. class:: warningmark | |
| 88 | |
| 89 While MIRA4 is aware of many read naming conventions to identify paired read | |
| 90 partners, the ``mirabait`` tool considers each read in isolation. Applying | |
| 91 it to paired read files may leave you with orphaned reads. | |
| 92 | |
| 93 | |
| 94 **Citation** | |
| 95 | |
| 96 If you use this Galaxy tool in work leading to a scientific publication please | |
| 97 cite the following papers: | |
| 98 | |
| 99 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
| 100 Galaxy tools and workflows for sequence analysis with applications | |
| 101 in molecular plant pathology. PeerJ 1:e167 | |
| 102 http://dx.doi.org/10.7717/peerj.167 | |
| 103 | |
| 104 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). | |
| 105 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. | |
| 106 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. | |
| 107 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html | |
| 108 | |
| 109 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 110 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler | |
| 111 </help> | |
| 112 </tool> |