<tool id="tree_species" name="tree_species" version="1.0">
  <description>Writes species not in a phylogeny to a text list.</description>
  <command interpreter="perl">
   tree_species.pl $infile $treefile > $outfile
  </command>
  <inputs>
    <param format="txt" name="infile" type="data" label="Full text list of species."/>
    <param format="txt" name="treefile" type="data" label="Tree to search. Newick format."/>
  </inputs>
  <outputs>
    <data format="txt" name="outfile" label="${tool.name} on ${on_string}: stdout" />
  </outputs>
    <help>
**What it does**

This tool can be used to determine which species from a list are not present in a tree.
Searches, one at a time, for species (OTUs) that are present in a tree file. If not found, the species is written to the output file.

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**Inputs**

1. A text list of species to use to search.
2. A phylogeny file.

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**Outputs**

A text list of species (OTU) names.

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**Additional Information**

This is a very simple perl script that just searches a text file for the presence of each line in the other file.

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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>