<tool id="tab2trees" name="tab2trees" version="1.0.0">
  <description>Create PDF file of phylogeny graphics from table of tree names and Newick trees</description>
  <command interpreter="bash">tab2trees.sh $input $output $treetype $extips $labeltax $Rfile $query $midpoint</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Dataset" help="First column=Tree Name. Second column=Newick phylogeny"/>
    <param name="treetype" type="select" label="Tree Plotting Style">
      <option value="phylogram">phylogram</option>
      <option value="cladogram">cladogram</option>
      <option value="fan">fan</option>
      <option value="unrooted">unrooted</option>
      <option value="radial">radial</option>
    </param>
    <param name='extips' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Exclude Tip Labels'/>
    <param name='query' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Highlight genes with QUERY and LANDMARK1 in name using Tip Label'/>
    <param format="tabular" name="labeltax" type="data" optional="true" label="Species to Mark File" help="Tab delimited file with 2 columns, gene, species. These will be marked on the trees." /> 
    <param name='midpoint' type='boolean' checked='true' truevalue='yes' falsevalue='no' label='Midpoint Root all Trees'/>
  </inputs>
  <outputs>
    <data format="txt" name="Rfile" />
    <data format="pdf" name="output" />
  </outputs>

  <help>
**What it does**

Creates a "book" of multiple phylogenetic tree graphics, one per page, in pdf format.

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**Inputs**

tab delimited file. Column 1 is tree name column 2 is newick tree string.

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**Outputs**

PDF file of phylogeny graphics.

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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>