<?xml version="1.2.1"?>
<tool name="Branch Lengths" id="hyphy_branch_lengths_wrapper1">
	
	<description>Estimation</description>
	
	<command interpreter="python">hyphy_branch_lengths_wrapper.py $input1 $out_file1 "$tree" "$model" "$base_freq" "Global" ${GALAXY_DATA_INDEX_DIR}</command>
	
    <inputs>
        <page>
            <param format="fasta" name="input1" type="data" label="Fasta file"/>
            <param name="tree" type="text" label="Tree Definition" size="20" help="For example: ((hg17,panTro1),(mm5,rn3),canFam1)"/>
            <param name="model" type="select" label="Substitution Model">
      	        <option value="000000">F81</option>
                <option value="010010">HKY85</option>
                <option value="012345">REV</option>
            </param>
<!--            <param name="model_options" type="select" label="Model Options">
      	        <option value="Local">All model parameters are estimated independently for each branch</option>
                <option value="Global">Model parameters are shared by all branches, branch lengths are estimated independently</option>
                <option value="Global w/variation">Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters are estimated</option>
                <option value="Global w/variation+HM">Model parameters are shared by all branches, branch lengths come from a user-chosen distribution, whose parameters is estimated; rates at adjacent sites are correlated via a simple Hidden Markov model with an autocorrelation parameter lambda</option>
            </param> -->
            <param name="base_freq" type="select" label="Base Frequencies">
      	        <option value="Observed">Nucleotide frequencies collected from the data file will be used as equilibrium frequencies</option>
                <option value="Equal">Equal (.25) frequencies are used as equilibrium frequencies</option>
            </param>
        </page>
    </inputs>
	<outputs>
		<data name="out_file1" format="tabular" />
	</outputs>
    <tests>
      <test>
        <param name="input1" value="branchlength_in.fasta"/>
        <param name="tree" value="((hg17,panTro1),(mm5,rn3),canFam1)"/>
        <param name="model" value="012345"/>
        <param name="base_freq" value="Observed"/>
        <output name="out_file1" file="branchlength_out.tabular"/>
      </test>
    </tests>
	<help>
This tool takes a single or multiple FASTA alignment file and estimates branch lengths using HYPHY_, a maximum likelihood analyses package.

For the tree definition, you only need to specify the species build names. For example, you could use the tree *((hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like this::

    &gt;hg17.chr7(+):26907301-26907310|hg17_0
    GTGGGAGGT
    &gt;panTro1.chr6(+):28037319-28037328|panTro1_0
    GTGGGAGGT
    &gt;mm5.chr6(+):52104022-52104031|mm5_0
    GTGGGAGGT
    &gt;rn3.chr4(+):80734395-80734404|rn3_0
    GTGGGAGGT
    &gt;canFam1.chr14(+):42826409-42826418|canFam1_0
    GTGGGAGGT

    &gt;hg17.chr7(+):26907310-26907326|hg17_1
    AGTCAGAGTGTCTGAG
    &gt;panTro1.chr6(+):28037328-28037344|panTro1_1
    AGTCAGAGTGTCTGAG
    &gt;mm5.chr6(+):52104031-52104047|mm5_1
    AGTCAGAGTGTCTGAG
    &gt;rn3.chr4(+):80734404-80734420|rn3_1
    AGTCAGAGTATCTGAG
    &gt;canFam1.chr14(+):42826418-42826434|canFam1_1
    AGTCAGAGTGTCTGAG

    &gt;hg17.chr7(+):26907326-26907338|hg17_2
    GTAGAAGACCCC
    &gt;panTro1.chr6(+):28037344-28037356|panTro1_2
    GTAGAAGACCCC
    &gt;mm5.chr6(+):52104047-52104059|mm5_2
    GTAGACGATGCC
    &gt;rn3.chr4(+):80734420-80734432|rn3_2
    GTAGATGATGCG
    &gt;canFam1.chr14(+):42826434-42826446|canFam1_2
    GTAGAAGACCCC

    &gt;hg17.chr7(+):26907338-26907654|hg17_3
    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
    &gt;panTro1.chr6(+):28037356-28037672|panTro1_3
    GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
    &gt;mm5.chr6(+):52104059-52104375|mm5_3
    GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
    &gt;rn3.chr4(+):80734432-80734748|rn3_3
    GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC
    &gt;canFam1.chr14(+):42826446-42826762|canFam1_3
    GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
    


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