<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13">
    <description>Build database from a FASTA file</description>
    <requirements>
        <requirement type="package" version="0.6.13">diamond</requirement>
    </requirements>
    <command>
    <!-- DB has two files, *.dmnd and *.tx -->
<![CDATA[
    diamond makedb 
        --threads "\${GALAXY_SLOTS:-12}"
        --in $infile
        --db ./database
    &&
    mv ./database.dmnd $outfile
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
    </inputs>

    <outputs>
        <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="protein.fasta" ftype="fasta"/>
            <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What it does**

DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
times faster than BLASTX, finding more than 94% of all matches.

.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/


]]>
    </help>
    <citations>
        <citation type="doi">10.1038/nmeth.3176</citation>
    </citations>
</tool>