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<tool id="phytab_raxml" name="Phytab RAxML" version="1.1">
  <description> for phytab input</description>
  <requirements>
    <requirement type="package">raxml</requirement>
  </requirements>
  <command interpreter="python">
    phytab_raxml.py -i $sequence -e $evo -f $efile -T 4 > $stdout 2>&amp;1 
  </command>
<!-- if using a queuing system, make sure number of ppn in jobrunner matches threads as set above -->
  <inputs>
    <param format="tabular" name="sequence" type="data" label="PHYTAB sequence file"/>
    <param name="evo" type="select" format="txt">
      <label>Model of evolution to apply to all data partitions (-m)</label>
      <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
    </param>
    <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab-delimited file with partition name in first column, evolutionary model in the second column. Must be RAxML 
valid model names. (optional)"/>
  </inputs>
  <outputs>
    <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**
Accepts Phytab input file (one or multiple gene partitions).  Runs RAxML using specified model or model file for each partition.  

For phytab format description, see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

See RAxML for additional information: https://github.com/stamatak/standard-RAxML

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**Performance**
The extent to which runs are parallelized may be altered through the Galaxy jobrunner (command-line). The number of threads is set in this tool's XML command section.

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Please direct questions or comments to [e-mail] 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>