<?xml version="1.1.1"?>
<tool name="dN/dS Ratio" id="hyphy_dnds_wrapper1">
	
	<description>Estimation</description>
	
	<command interpreter="python">hyphy_dnds_wrapper.py $input1 $out_file1 "$tree" "$model" $analysis ${GALAXY_DATA_INDEX_DIR}</command>
	
    <inputs>
        <page>
            <param format="fasta" name="input1" type="data" label="Fasta file"/>
            <param name="analysis" type="select" label="Analysis to run on every gene">
      	    	<option value="global">Global</option>
      	        <option value="local">Local</option>
            </param>
            <param name="tree" type="text" label="Tree Definition in Newick format" 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>
        </page>
    </inputs>
	<outputs>
		<data name="out_file1" format="tabular" />
	</outputs>
    <tests>
      <test>
        <param name="input1" value="dnds_inp.fasta"/>
        <param name="tree" value="((human, chimp), mouse)"/>
        <param name="model" value="000000"/>
        <param name="analysis" value="global"/>
        <output name="out_file1" file="dnds_out.tabular"/>
      </test>
    </tests>
	<help>

.. class:: infomark

This tool takes a FASTA alignment file and estimates dN/dS ratio using HYPHY_, a maximum likelihood analyses package.

-----

.. class:: warningmark

The tool returns an error message if no tree definition or an invalid tree definition is supplied. 
Any block/s not containing as many species as mentioned in the tree definition will be omitted from the output.

-----

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 the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition::

    &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>