<tool id="long_branch_finder" name="Long Branch Finder" version="1.0">
  <description>Identifies long tips in newick trees</description>
  <command interpreter="python">long_branch_finder.py $tabulartreelist $cutoffvalue > $output</command>
  <inputs>
    <param name="tabulartreelist" format="tabular" type="data" label="Tabulated list of newick trees with branch lengths" help="See format requirements and restrictions below. This input will be list of trees output from Phytab RAxML-Parsimony"/>
    <param name="cutoffvalue" size="4" type="integer" value="1" label="Identify tips longer than ___ standard deviations of the tree's median branch length" help="Enter an integer as the cut-off."/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="${tool.name} on ${on_string}: Long-tips list" />
  </outputs>
  <help>

**What it does**

Use this tool to create a list of terminal branches from one or more trees that exceed a length cut-off.  

This tool calculates the statistics for the branch-length distribution in each newick tree.  A terminal branch whose length falls past a specified number of standard deviations is reported in 
the output.
The list output from this tool may be used to filter/prune the original PHYTAB sequence file using the tool "Prune phytab using list".

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**Example**

Input File (2 tab-delimited columns)::

  GeneA   (((Felis_catus:0.234,Canis_familiaris:0.345):0.567,Equus_monoclonius:3.98):0.564,Mus_musculus:0.456):0.0;
  GeneB   (((Felis_catus:4.123,Canis_familiaris:0.035):0.234,Equus_monoclonius:1.12):0.345,Mus_musculus:0.234):0.0;

Currently, taxon names must only include only alphanumeric characters in two fields delimted by one underscore, for example: 

  Genus_species
  GENUSspecies_sample2010

If 3 standard deviations are selected as the cut-off, then the output from the example above will yield::

  Equus_monoclonius  geneA
  Felis_catus  geneB

Only terminal branches will be identified.  (To remove entire clades subtended by long internal branches, see the tool "phytab_LB_pruner".)

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**Additional Information**

Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org
   
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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
  </help>
</tool>