<tool id="blast_parser" name="BLAST parser" version="0.2.0">
    <description>
        Convert 12- or 24-column BLAST output into 3-column hcluster_sg input
    </description>
    <requirements>
        <requirement type="package" version="3.13">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
<![CDATA[
python3 '$__tool_directory__/blast_parser.py'
-i '$input'
-o '$output'
#if $reciprocal
    -r
#end if
]]>
    </command>

    <inputs>
        <param name="input" type="data" format="tabular" label="Tabular data" help="BLAST 12 column tabular format data"/>
        <param name="reciprocal" type="boolean" checked="false" label="Reciprocal results" help="returns only reciprocal results"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="$tool.name on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="input" ftype="tabular" value="input.tabular" />
            <param name="reciprocal" value="false" />
            <output name="output" file="output.tabular" />
        </test>
        <test>
            <param name="input" ftype="tabular" value="input.tabular" />
            <param name="reciprocal" value="true" />
            <output name="output" file="output2.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
Simple tool to convert a 12- or 24-column BLAST output into a 3-column format (qseqid, sseqid, round(-1 * log10(evalue)/2)) usable as input for the hcluster_sg tool.
]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
    </citations>
</tool>