<tool id="tn93_filter" name="TN93 Filter" version="@TOOL_VERSION@+galaxy0">
    <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.84">biopython</requirement>
    </expand>
    <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" min="0" max="1" 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
----

This is a simple program meant to compute pairwise distances between aligned 
nucleotide sequences in sequential FASTA format using the 
[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).

USAGE
-----

    usage: tn93 [-h] [-o OUTPUT] [-t THRESHOLD] [-a AMBIGS] [-l OVERLAP][-d COUNTS_IN_NAME] [-f FORMAT] [-s SECOND_FASTA] [-b] [-c] [-q] [FASTA]

Try it from using the example file in 'data' by typing 

    tn93 -t 0.05 -o data/test.dst data/test.fas

Output (diagnostics written to stderr, histogram written to stdout so can be redirected)

Example:

    Read 8 sequences of length 1320
    Will perform 28 pairwise distance calculations
    Progress:     100% (       7 links found,          inf evals/sec)
    {
        "Actual comparisons performed" :28,
        "Total comparisons possible" : 28,
        "Links found" : 7,
        "Maximum distance" : 0.0955213,
        "Mean distance" : 0.0644451,
        "Histogram" : [[0.005,0],[0.01,0],[0.015,0],[0.02,0],[0.025,0],[0.03,2],[0.035,1],[0.04,0],[0.045,1],[0.05,3],[0.055,1],[0.06,2],[0.065,2],[0.07,3],[0.075,4],[0.08,3],[0.085,3],[0.09,2],[0.095,0],[0.1,1],[0.105,0],[0.11,0],[0.115,0],[0.12,0],[0.125,0],[0.13,0],[0.135,0],[0.14,0],[0.145,0],[0.15,0],[0.155,0],[0.16,0],[0.165,0],[0.17,0],[0.175,0],[0.18,0],[0.185,0],[0.19,0],[0.195,0],[0.2,0],[0.205,0],[0.21,0],[0.215,0],[0.22,0],[0.225,0],[0.23,0],[0.235,0],[0.24,0],[0.245,0],[0.25,0],[0.255,0],[0.26,0],[0.265,0],[0.27,0],[0.275,0],[0.28,0],[0.285,0],[0.29,0],[0.295,0],[0.3,0],[0.305,0],[0.31,0],[0.315,0],[0.32,0],[0.325,0],[0.33,0],[0.335,0],[0.34,0],[0.345,0],[0.35,0],[0.355,0],[0.36,0],[0.365,0],[0.37,0],[0.375,0],[0.38,0],[0.385,0],[0.39,0],[0.395,0],[0.4,0],[0.405,0],[0.41,0],[0.415,0],[0.42,0],[0.425,0],[0.43,0],[0.435,0],[0.44,0],[0.445,0],[0.45,0],[0.455,0],[0.46,0],[0.465,0],[0.47,0],[0.475,0],[0.48,0],[0.485,0],[0.49,0],[0.495,0],[0.5,0],[0.505,0],[0.51,0],[0.515,0],[0.52,0],[0.525,0],[0.53,0],[0.535,0],[0.54,0],[0.545,0],[0.55,0],[0.555,0],[0.56,0],[0.565,0],[0.57,0],[0.575,0],[0.58,0],[0.585,0],[0.59,0],[0.595,0],[0.6,0],[0.605,0],[0.61,0],[0.615,0],[0.62,0],[0.625,0],[0.63,0],[0.635,0],[0.64,0],[0.645,0],[0.65,0],[0.655,0],[0.66,0],[0.665,0],[0.67,0],[0.675,0],[0.68,0],[0.685,0],[0.69,0],[0.695,0],[0.7,0],[0.705,0],[0.71,0],[0.715,0],[0.72,0],[0.725,0],[0.73,0],[0.735,0],[0.74,0],[0.745,0],[0.75,0],[0.755,0],[0.76,0],[0.765,0],[0.77,0],[0.775,0],[0.78,0],[0.785,0],[0.79,0],[0.795,0],[0.8,0],[0.805,0],[0.81,0],[0.815,0],[0.82,0],[0.825,0],[0.83,0],[0.835,0],[0.84,0],[0.845,0],[0.85,0],[0.855,0],[0.86,0],[0.865,0],[0.87,0],[0.875,0],[0.88,0],[0.885,0],[0.89,0],[0.895,0],[0.9,0],[0.905,0],[0.91,0],[0.915,0],[0.92,0],[0.925,0],[0.93,0],[0.935,0],[0.94,0],[0.945,0],[0.95,0],[0.955,0],[0.96,0],[0.965,0],[0.97,0],[0.975,0],[0.98,0],[0.985,0],[0.99,0],[0.995,0],[1,0]]
    }
    
NOTES
-----

All sequences must be aligned and have the same length.  Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in 

    >seqname:10

':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers 
only affect histogram and mean calculations.
]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
    </expand>
</tool>