<tool id="phytab_clearcut" name="phytab clearcut" version="1.0.0">
  <description>clearcut: Generate Neighbor Joining phylogeny. Input can be aligned fasta or phytab format.</description>
  <requirements>
    <requirement type="package">clearcut</requirement>
  </requirements>
  <command interpreter="python">
    phytab_clearcut.py -i $data -t $datatype > $clearcut_stdout 2>&amp;1
  </command>
  <inputs>
    <param format="tabular" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or fasta"/>
    <param name="datatype" type="select" format="text">
      <label>Type of data for all partitions</label>
      <option value="P">Protein</option> 
	<option value="D">DNA</option> 
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="clearcut_stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="clearcut_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" />
  </outputs>
  <tests>
  </tests>
<help>
**What it does**

This tool uses the the program Clearcut to infer a Neighbor-Joining phylogeny using the fast RNJ algorithm for a data set using uncorrected distances (p-distances).

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**Input**
The program will automatically detect possible inputs of two types
1. ALIGNED FASTA file for a single gene family

2. ALIGNED PHYTAB for multiple genes. See 
http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html for description of phytab format.

------

**Output**

A phylogenetic tree in newick format. In the Osiris package this can be visualized with a tool like TreeVector.

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**Additional Information**

http://bioinformatics.hungry.com/clearcut/

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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

Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining: A Fast Distance-Based Phylogenetic Tree Construction Method, J. Mol. Evol., 62, 785-792

</help>
</tool>