<tool id="tn93_filter" name="TN93 Filter" version="@VERSION@">
    <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">tn93</requirement>
        <requirement type="package" version="1.70">biopython</requirement>
    </requirements>
    <version_command><![CDATA[tn93 --version]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    cat '$reads' > filtered_msa.fa &&
    tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' &&
    python '$__tool_directory__/tn93_filter.py' --reference '$reference'
        --distances pairwise.csv
        --reads filtered_msa.fa
        --clusters '$clusters'
    ]]></command>
    <inputs>
        <param name="reads" type="data" format="fasta" label="Aligned reads" />
        <param name="reference" type="data" format="fasta" label="Reference sequence" />
        <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" />
        <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" />
    </inputs>
    <outputs>
        <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" />
    </outputs>
    <tests>
        <test>
            <param name="reads" value="filter-in1-reads.fa" />
            <param name="reference" value="filter-in1-reference.fa" />
            <param name="clusters" value="filter-in1-clusters.fa" />
            <param name="threshold" value="0.35" />
            <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[
TN93-Filter
===========

Removes aligned sequences that are within a given distance from a reference
sequence using the 1993 Tamura-Nei distance calculation.
]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
    </expand>
</tool>