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<tool id="raxml_pars" name="raxml_pars" version="1.0.0" force_history_refresh='True'>
    <description> Use RAxML to calculate a phylogeny with Parsimony </description>
    <requirements>
        <requirement type="package">raxml</requirement>
    </requirements>
    <command interpreter="perl">
        raxml_pars.pl $datatype $data_file $part_file 
		$seed $Out  > $raxml_log
			2>&amp;1
    </command>
    <inputs>
        <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/>
	<param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/>
    <param name="datatype" type="select" label="Data Type" help="If you have multiple, mixed data types, specify them in a partition file ">
      <option value="PROTGAMMAWAG">PROTEIN</option>
      <option value="GTRGAMMA">DNA</option>
      <option value="BINGAMMA">BINARY</option>
      <option value="MULTIGAMMA">Multistate Morphology</option>
    </param>
	<param name="seed" type="integer" value="1234567" label="Random Number Seed for search"/>
        <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/>
	<param name="Run" type="text" label="Run Name" help="For Galaxy History"/>
    </inputs>
    <outputs>
	<data format="txt" name="raxml_log" label="$Run: ${tool.name} Screen Output on ${on_string}" />
        <data format="txt" name="raxml_info" label="$Run: ${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.parsimony" />
        <data format="txt" name="best_trees" label="$Run: ${tool.name} MP Tree ${on_string}" from_work_dir="RAxML_parsimonyTree.parsimony" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

RAxML_pars estimates phylogenetic trees, in this case calling a Parsimony algorithm.

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**Inputs**

Input file is a RAxML compatible text file. This can be generated by Osiris tools from an aligned fasta file with fasta2phylipE or from a PHYTAB format file with phylocatenator.

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**Outputs**

RAxML writes the resulting tree file in newick text format, which can be viewed in Osiris with TreeVector (of the mothur package).

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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

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>