<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.3">
    <description>Filter reads using kmer matches</description>
    <requirements>
        <requirement type="binary">mirabait</requirement>
        <requirement type="package" version="4.0">MIRA</requirement>
    </requirements>
    <version_command interpreter="python">mira4_bait.py --version</version_command>
    <command interpreter="python">
mira4_bait.py $input_reads.ext $output_choice $strand_choice $kmer_length $min_occurence "$bait_file" "$input_reads" "$output_reads"
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="bait_file" type="data" format="fasta,fastq,mira" required="true" label="Bait file (what to look for)" />
        <param name="input_reads" type="data" format="fasta,fastq,mira" required="true" label="Reads to search" />
        <param name="output_choice" type="select" label="Output positive matches, or negative matches?">
            <option value="pos">Just positive matches</option>
            <option value="neg">Just negative matches</option>
        </param>
        <param name="strand_choice" type="select" label="Check for matches on both strands?">
            <option value="both">Check both strands</option>
            <option value="fwd">Just forward strand</option>
        </param>
        <param name="kmer_length" type="integer" value="31" min="1" max="32"
               label="k-mer length" help="Maximum 32" />
        <param name="min_occurence" type="integer" value="1" min="1"
               label="Minimum k-mer occurence"
               help="How many k-mer matches do you want per read? Minimum one" />
    </inputs>
    <outputs>
        <data name="output_reads" format="input" metadata_source="input_reads"
	      label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
            <output name="output_reads" file="tvc_mini_bait_pos.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
            <param name="kmer_length" value="32" />
            <param name="min_occurence" value="50" />
            <output name="output_reads" file="tvc_mini_bait_strict.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="bait_file" value="tvc_bait.fasta" ftype="fasta" />
            <param name="input_reads" value="tvc_mini.fastq" ftype="fastqsanger" />
            <param name="output_choice" value="neg" />
            <output name="output_reads" file="tvc_mini_bait_neg.fastq" ftype="fastqsanger" />
        </test>
    </tests>
    <help>
**What it does**

Runs the ``mirabait`` utility from MIRA v4.0 to filter your input reads
according to whether or not they contain perfect kmer matches to your
bait file. By default this looks for 31-mers (kmers or *k*-mers where
the fragment length *k* is 31), and only requires a single matching kmer.

The ``mirabait`` utility is useful in many applications and pipelines
outside of using the main MIRA tool for assembly or mapping.

.. class:: warningmark

Note ``mirabait`` cannot be used on protein (amino acid) sequences.

**Example Usage**

To remove over abundant entries like rRNA sequences, run ``mirabait`` with
known rRNA sequences as the bait and select the *negative* matches.

To do targeted assembly by fishing out reads belonging to a gene and just
assemble these, run ``mirabait`` with the gene of interest as the bait and
select the *positive* matches.

To iteratively reconstruct mitochondria you could start by fishing out reads
matching any known mitochondrial sequence, assembly those, and repeat.


**Notes on paired read**

.. class:: warningmark

While MIRA4 is aware of many read naming conventions to identify paired read
partners, the ``mirabait`` tool considers each read in isolation. Applying
it to paired read files may leave you with orphaned reads.


**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
    </help>
</tool>