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<tool id="SHtest" name="SHtest" version="1.0.0" force_history_refresh='True'>
    <description> Use RAxML to calculate SHtest to compare phylogenetic tree topologies 
    </description>
    <requirements>
        <requirement type="package">raxml</requirement>
    </requirements>
    <command interpreter="perl">
        SHtest.pl $datatype $data_file $part_file $best_tree $alt_trees
		  > $raxml_log
			2>&amp;1
    </command>
    <inputs>
        <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
    <param name="datatype" type="select" format="text">
      <label>Model of evolution to apply to all data partitions (-m)</label>
      <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
    </param>
        <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
        <param format="txt" name="best_tree" type="data" optional="true" label="ML Tree" help="ML Tree in newick format."/>
        <param format="txt" name="alt_trees" type="data" optional="true" label="Alt Tree(s)" help="Alternative Hypothesis Tree(s) in newick format."/>
    </inputs>
    <outputs>
	<data format="txt" name="raxml_log" label="${tool.name} Screen Output on ${on_string}" />
        <data format="txt" name="raxml_info" label="${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.SH" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

SHtest performs the Shimodaira-Hasegawa statistical test to compare one tree topology to alternative tree(s). The test is implemented with RAxML.

------

**Inputs**

#. A file in RAxML (phylipE) format. This can be made with Osiris tools phylocatenator or fasta2phylipE. 
#. Model of evolution assumed for likelihood calculations.
#. An optional RAxML partition file delineates data set partitions. This can be made with Osiris tool phylocatenator.
#. Target phylogeny in newick format.
#. Alternative hypothesis phylogenetic tree(s) in newick format.

------

**Outputs**

The output is text output from RAxML, which details the statistical value of the SH test(s).

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**Additional Information**

raxml Home Page:
http://www.exelixis-lab.org/software.html
   
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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

Shimodaira H., M. Hasegawa, 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol 16:1114-1116

Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics.
http://bioinformatics.oxfordjournals.org/content/22/21/2688.short

    </help>
</tool>