<tool id="augur_align" name="augur align" version="@TOOL_VERSION@+galaxy0">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">augur</requirement>
    </requirements>
    <version_command>augur --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        augur align
          --nthreads \${GALAXY_SLOTS:-1}
          --sequences '$sequences'
          --reference-sequence '$reference_sequence'
          $fill_gaps
          --output 'output'
    ]]></command>
    <inputs>
        <param name="sequences" type="data" format="fasta" label="Sequences"/>
        <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence"/>
        <param name="fill_gaps" type="boolean" checked="false" truevalue="--fill-gaps" falsevalue="" label="Fill Gaps"/>
    </inputs>
    <outputs>
        <data name="pre_aligner_output" format="fasta" >
            <discover_datasets pattern="output.pre_aligner.fasta" format="fasta" visible="true" />
        </data>
        <data name="post_aligner_output" format="fasta" >
            <discover_datasets pattern="output.post_aligner.fasta" format="fasta" visible="true" />
        </data>
        <data name="log" format="text" >
            <discover_datasets pattern="*.log" format="text" visible="true" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="sequences" value="augur_align_test_0_sequences.input.fasta" />
            <param name="reference_sequence" value="augur_align_test_0_reference_sequence.input.fasta" />
	    <param name="fill_gaps" value="false" />
            <output name="pre_aligner_output" file="augur_align_test_0_pre_aligner_output.output.fasta" />
            <output name="post_aligner_output" file="augur_align_test_0_post_aligner_output.output.fasta" />
        </test>
    </tests>
    <help><![CDATA[
Align multiple sequences from FASTA or VCF.
    ]]></help>
    <expand macro="citations" />
</tool>