<tool id="bbmap_sendsketch" name="bbmap_sendsketch" version="39.26+galaxy25">
    <description> Identifying species using sketch</description>
    <requirements>
      <requirement type="package" version="39.37">bbmap</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re
        #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
        ln -sf '$input' '$safename' &&
        sendsketch.sh
        #if $printall
            printall=t
        #end if
        #if $translate
            translate=t
        #end if
        in='$safename'
        out=output.txt
        outsketch=sketch
        minhits=$minhits
        minani=$minani
        format=$format
        score=t
        $db
    ]]>    </command>

    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="Input sequence"/>
        <param name="db" type="select" label="Sketch Database">
            <option value="refseq" selected="true">Refseq</option> 
            <option value="nt">nt</option> 
            <option value="silva">silva</option> 
            <option value="protein">RefSeq prokaryotic amino acid sketches</option> 
        </param>
        <param name="format" type="select" label="Output Format">
            <option value="2" selected="true">Default format with, per query, one query header line;
                   one column header line; and one reference line per hit</option>
            <option value="3">One line per hit, with columns query, reference, ANI,
                   and sizeRatio</option>
            <option value="4">JSON</option>
        </param>
        <param name="minhits" type="integer" min="1" value="3" label="Only report records with at least this many hits"/>
        <param name="minani" type="float" min="0" value="0.0" max="1" label="Only report records with at least this ANI"/>
        <param name="minwkid" type="float" min="0" value="0.0001" max="1" label="Only report records with at least this WKID"/>
        <param name="minbases" type="integer" min="0" value="0" label="Ignore ref sketches of sequences shortert than this"/>
        <param name="minsizeratio" type="float" min="0" value="0.0" max="1" label="Don't compare sketches if the smaller genome is less than
                this fraction of the size of the larger"/>
        <param name="records" type="integer" min="1" value="20" label="Report at most this many best-matching records"/>
        <param name="write_sketch" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Write sketch?"/>
        <param name="translate" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Call genes and translate to proteins.  Input should be
                nucleotides"/>
        <param name="printall" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Print all column?"/>
    </inputs>

    <outputs>
        <data name="Output" format="txt" label="${tool.name} on ${on_string} Results" from_work_dir="output.txt"/>
        <data name="Sketch" format="binary" label="${tool.name} on ${on_string} Sketch" from_work_dir="sketch">
            <filter>write_sketch is True</filter>
        </data>
    </outputs>
    <help><![CDATA[
    Compares query sketches to reference sketches hosted on a
    remote server via the Internet.  The input can be sketches made by sketch.sh,
    or fasta/fastq files from which SendSketch will generate sketches.
    Only sketches will sent, not sequences.
    ]]>    </help>
    <expand macro="citations" />

</tool>