<tool id="presto_alignsets" name="pRESTO AlignSets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Multiple-align sequences with the same barcodes.</description>
    <macros>
        <import>presto_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    
    <expand macro="requirements"/>
    
    <version_command>AlignSets.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$fastq_in' in.fastq &&
        AlignSets.py muscle
          --nproc "\${GALAXY_SLOTS:-1}"
          -s in.fastq
          --bf '$bf'
          $div
          --outname=tmp
          #if $capture_log
            --log '$log_out'
          #end if
    ]]></command>

    <inputs>
        <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
        <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
        <param argument="--div" type="boolean" value="false" truevalue="--div" falsevalue="" label="Calculate Nucleotide Diversity" help="Specify to calculate nucleotide diversity of each set."/>
        <expand macro="presto-log-param"/>
    </inputs>

    <outputs>
        <data name="fastq_out" format="fastq" from_work_dir="tmp_align-pass.fastq"/>
        <expand macro="presto-log-output"/>
    </outputs>
    
    <tests>
        <test expect_num_outputs="2">
            <param name="fastq_in" value="presto_alignsets_test_in.fastq"/>
            <param name="capture_log" value="true"/>
            <output name="fastq_out" file="presto_alignsets_test_out.fastq" compare="sim_size" delta="15"/>
            <output name="log_out">
                <assert_contents>
                    <has_text text="SEQCOUNT"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
Multiple aligns sequences with the same barcode to correct for any misalignments due to either different primer usage or insertions/deletions in the sequences.

Only supports the "muscle" sub-command of pRESTO's AlignSets.py.

See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.

@HELP_NOTE@
    ]]></help>
    <expand macro="citations" />
</tool>