<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@">
    <description>Build database from a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />

    <command>
    <!-- DB has two files, *.dmnd and *.tx -->
<![CDATA[
    diamond makedb
        --threads "\${GALAXY_SLOTS:-12}"
        --in '$infile'
        --db ./database
]]>
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
    </inputs>

    <outputs>
        <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="db.fasta" ftype="fasta"/>
            <output name="outfile" value="db.dmnd"/>
        </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 is about 2,500
times faster than BLASTX, finding more than 94% of all matches.

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


]]>
    </help>

    <expand macro="citations" />
</tool>