<tool id="gd_raxml" name="RAxML" version="1.0.0">
  <description>: construct a maximum-likelihood phylogenetic tree</description>

  <command interpreter="python">
    raxml.py '$input' '$output'
  </command>

  <inputs>
    <param name="input" type="data" format="txt" label="PHYLIP dataset" />
  </inputs>

  <outputs>
    <data name="output" format="nhx" />
  </outputs>


  <requirements>
    <requirement type="package" version="7.7.6">raxml</requirement>
  </requirements>

  <help>
**What it does**

This tool runs RAxML on a phylip formatted file and returns a maximum
likelihood phylogram supported by a desired number of bootstraps.

This program takes as input a phylip formatted file and optionally a
number of parameters (for further information consult the manual_),
and returns a Newick formatted tree that can be explored with Phyloviz.

By default the program runs 1,000 fast bootstraps on the best likelihood
tree constructed with the GRT + gamma model.

.. _manual: http://sco.h-its.org/exelixis/oldPage/RAxML-Manual.7.0.4.pdf

  </help>
</tool>