<?xml version="1.1.1"?>
<tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1">
    
    <description>Builder</description>
    
    <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric ${GALAXY_DATA_INDEX_DIR}</command>
    
    <inputs>
        <page>
            <param format="fasta" name="input1" type="data" label="Fasta file"/>
            <param name="distance_metric" type="select" label="Distance Model">
                  <option value="TN93">Tamura-Nei (93)</option>
                <!-- <option value="TN93_RV">Tamura-Nei (93) distance and rate variation (unequal character frequencies, A->G, C->T and transversional bias corrections, gamma distributed rate variation from site to site)</option> -->
                <!-- <option value="TN84">Tajima-Nei (84) distance (unequal character frequencies)</option> -->
                <!-- <option value="K2P_RV">Kimura 2 parameter and rate variation (equal character frequencies, transition/trasversion bias correction, gamma distributed rate variation from site to site)</option> -->
                <option value="K2P">Kimura 2 parameter</option>
                <option value="JC69">Jukes-Cantor</option>
                <!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> -->
                <!-- <option value="p_Distance">Number of observed substitutions per site</option> -->
                <!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> -->
                <!-- <option value="Unaligned_LZ_FR">Distance measure for unaligned sequences based on Lempel Ziv measure of information content using the best choice forward and reverse string orientations</option> -->
            </param>
        </page>
    </inputs>
    <outputs>
        <data name="out_file1" format="tabular" />
        <data name="out_file2" format="pdf" />
    </outputs>
    <requirements>
      <requirement type="binary">ps2pdf</requirement>
    </requirements>
    <tests>
      <test>
        <param name="input1" value="nj_tree_inp.fasta"/>
        <param name="distance_metric" value="TN93"/>
        <output name="out_file1" file="nj_tree_newick_out.tabular"/>
        <output name="out_file2" file="nj_tree_pdf_out.pdf"/> 
      </test>
    </tests>
    <help>
This tool takes a single or multiple FASTA alignment file and builds Neighbor Joining Trees using HYPHY_, a maximum likelihood analyses package.

.. _HYPHY: http://www.hyphy.org
    </help>
</tool>