<tool id="change_sp" name="change_sp" version="1.0">
    <description>Change code name to full species name in fasta or phytab</description>
    <command interpreter="perl">
		change_sp.pl $infile $changefile $outfile
    </command>
    <inputs>
	    <param name="infile" type="data" format="tabular" label="Input File" help="PHYTAB file to alter" />
	    <param name="changefile" type="data" format="tabular" label="Conversion Table" help="Tabular format with column 1=code; column 2=Full species name" />
    </inputs>
    <outputs>
	<data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>
**What it does**

Many times a dataset will have code names instead of full species names. This will search for a code name and replace with a species name based on a table of input values.

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**Inputs**

PHYTAB with species codes

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**Outputs**

PHYTAB with full species names replacing codes
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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>