<tool id="PDpairs" name="PDpairs">
    <description>Pairwise distance between taxa in a phylogenetic tree</description>
    <requirements>
	<requirement type="perl-module">Bio</requirement>
    </requirements>
    <command interpreter="perl">
		PD.pl $intable $intree $outtable $half
    </command>
    <inputs>
	    <param name="intree" type="data" format="txt" label="Input Tree File" help="newick" />
	    <param name="intable" type="data" format="tabular" label="Table of species pairs" help="species tab species" />
       	    <param name='half' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Calculate Divergence times (divides pairwise distances in half)' />
    </inputs>
    <outputs>
	<data format="tabular" name="outtable" label="${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>
**What it does**

PDpairs generates Phylogenetic Distances (PD) for pairs of species in a phylogenetic tree.

------

**Input formats**

Input a table of species pairs::

  species1	species2
  species2	species4

And a Newick format phylogeny with branch lengths

------

**Outputs**

Output is a table of the species pairs followed by a column of pairwise distance for each tree in the file::

  species1	species2	1.104
  species2	species4	2.119

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**Citations**   

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html

Additional Citations for this tool

Stajich, J., Block, D., Boulez, K., Brenner, S., Chervitz, S., Dagdigian, C., Fuellen, G., Gilbert, J., Korf, I., Lapp, H. et al. (2002). The Bioperl toolkit: perl modules for the life sciences. Genome Res. 12,1611 -1618.

Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61:1-10.

    </help>
</tool>