<tool id="extract_variants" name="Extract variant fragments" version="0.5.25">
    <description>from long reads</description>
    <requirements>
        <requirement type="package" version="0.5.25">readtagger</requirement>
    </requirements>
    <version_command>extract_variants --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
ln -fs '$insert_reference.fields.path' reference.fa &&
extract_variants '$input' '$output_alignment' reference.fa &&
summarize_fragments '$output_alignment' '$output_tabular'
    ]]></command>
    <inputs>
        <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
        <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select">
            <options from_data_table="all_fasta"/>
        </param>
    </inputs>
    <outputs>
        <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="long_insertion.bam" ftype="bam"/>
            <param name="insert_reference" value="transposon"/>
            <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
            <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

Extract variants will find soft-clipped alignments and alignments with insertions,
and, if the inserted sequence aligns with the selected reference, write out
a the alignment, but clip the aligned portion of the read to a single N
and will add 2 tags, AR and AD to the alignment.
The AR tag will list the contig, the AD tag contains detailed
information on how the insert/clipped sequence aligned against the selected
reference.
    ]]></help>
</tool>