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1 <tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.3">
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2 <description>Filter reads using kmer matches</description>
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3 <requirements>
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4 <requirement type="binary">mirabait</requirement>
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5 <requirement type="package" version="4.0">MIRA</requirement>
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6 </requirements>
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7 <version_command interpreter="python">mira4_bait.py --version</version_command>
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8 <command interpreter="python">
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9 mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads"
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10 </command>
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11 <stdio>
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12 <!-- Assume anything other than zero is an error -->
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13 <exit_code range="1:" />
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14 <exit_code range=":-1" />
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15 </stdio>
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16 <inputs>
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17 <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
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18 <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
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19 <param name="output_choice" type="select" label="Output positive matches, or negative matches?">
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20 <option value="pos">Just positive matches</option>
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21 <option value="neg">Just negative matches</option>
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22 </param>
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23 <param name="strand_choice" type="select" label="Check for matches on both strands?">
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24 <option value="both">Check both strands</option>
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25 <option value="fwd">Just forward strand</option>
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26 </param>
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27 <param name="kmer_length" type="integer" value="31" min="1" max="32"
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28 label="k-mer length" help="Maximum 32" />
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29 <param name="min_occurence" type="integer" value="1" min="1"
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30 label="Minimum k-mer occurence"
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31 help="How many k-mer matches do you want per read? Minimum one" />
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32 </inputs>
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33 <outputs>
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34 <data name="output_reads" format="input" metadata_source="input_reads"
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35 label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
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40 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
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41 <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
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42 </test>
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43 <test>
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44 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
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45 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
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46 <param name="kmer_length" value="32" />
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47 <param name="min_occurence" value="50" />
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48 <output name="output_reads" file="tvc_mini_bait_strict.fastq" ftype="fastqsanger" />
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49 </test>
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50 <test>
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51 <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
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52 <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
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53 <param name="output_choice" value="neg" />
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54 <output name="output_reads" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 Runs the ``mirabait`` utility from MIRA v4.0 to filter your input reads
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61 according to whether or not they contain perfect kmer matches to your
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62 bait file. By default this looks for 31-mers (kmers or *k*-mers where
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63 the fragment length *k* is 31), and only requires a single matching kmer.
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64
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65 The ``mirabait`` utility is useful in many applications and pipelines
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66 outside of using the main MIRA tool for assembly or mapping.
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67
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68 .. class:: warningmark
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69
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70 Note ``mirabait`` cannot be used on protein (amino acid) sequences.
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71
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72 **Example Usage**
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73
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74 To remove over abundant entries like rRNA sequences, run ``mirabait`` with
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75 known rRNA sequences as the bait and select the *negative* matches.
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76
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77 To do targeted assembly by fishing out reads belonging to a gene and just
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78 assemble these, run ``mirabait`` with the gene of interest as the bait and
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79 select the *positive* matches.
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80
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81 To iteratively reconstruct mitochondria you could start by fishing out reads
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82 matching any known mitochondrial sequence, assembly those, and repeat.
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83
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84
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85 **Notes on paired read**
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86
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87 .. class:: warningmark
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88
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89 While MIRA4 is aware of many read naming conventions to identify paired read
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90 partners, the ``mirabait`` tool considers each read in isolation. Applying
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91 it to paired read files may leave you with orphaned reads.
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92
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93
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94 **Citation**
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95
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96 If you use this Galaxy tool in work leading to a scientific publication please
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97 cite the following papers:
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98
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99 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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100 Galaxy tools and workflows for sequence analysis with applications
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101 in molecular plant pathology. PeerJ 1:e167
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102 http://dx.doi.org/10.7717/peerj.167
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103
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104 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
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105 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
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106 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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107 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
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108
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109 This wrapper is available to install into other Galaxy Instances via the Galaxy
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110 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
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111 </help>
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112 </tool>
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