<tool id="blast_unmatched" name="Blast Unmatched" version="1.0.1">
    <description>get query sequences that didn't get a match during a blast</description>
    <requirements>
        <requirement type="package" version="3.7.6">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__'/blast_unmatched.py
            --fasta $fasta_file
            --blast $blast_file
            --output $output_file
    ]]></command>
    <inputs>
        <param type="data" name="fasta_file" format="fasta"/>
        <param type="data" name="blast_file" format="tabular"/>
    </inputs>
    <outputs>
        <data name="output_file" format="fasta" label="Unmatched queries from blast: ${blast_file.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="blast_file" value="test_blast.tab"/>
            <param name="fasta_file" value="test_query.fa"/>
            <output name="output_file" ftype="fasta" file="test_output.fa"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool takes a `blast`_ output in tabular format(with the query id in 1rst column) and the fasta file used as query. It then return the query sequences that remained unmatched during the blast.

.. _blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi

    ]]></help>
    <citations>
        <citation type="doi">10.1186/s13742-015-0080-7</citation>
    </citations>
</tool>