<tool id="make_phylogeny" name="make_phylogeny" version="1.2.0">
 <description>Make Phylogeny</description>
 <requirements>
  <requirement type="binary">make_phylogeny.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  make_phylogeny.py
  --input_fp=$input_fp
  --tree_method=$tree_method
  --root_method=$root_method
  --result_fp=$result_fp
  --log_fp=$log_fp
 </command>
 <inputs>
  <param name="input_fp" type="data" format="align" label="input_fp"
   help="Path to read input alignment [REQUIRED]"/>
  <param name="tree_method" type="select" label="tree_method"
   help="Method for tree building. Valid choices are: clearcut, clustalw, raxml, fasttree_v1, fasttree, muscle [default: fasttree]">
    <option value="clearcut">clearcut</option>
    <option value="clustalw">clustalw</option>
    <option value="raxml">raxml</option>
    <option value="fasttree_v1">fasttree_v1</option>
    <option value="fasttree" selected="true">fasttree</option>
    <option value="muscle">muscle</option>
  </param>
  <param name="root_method" type="select" label="root_method"
   help="method for choosing root of phylo tree  Valid choices are: midpoint, tree_method_default [default: tree_method_default]">
    <option value="tree_method_default" selected="true">tree_method_default</option>
    <option value="midpoint">midpoint</option>
  </param>
 </inputs>
 <outputs>
  <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
  <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>