<tool id="fasta2phytab" name="FASTA2PHYTAB" version="1.1">
    <description>Converts FASTA file with sequences from same gene family to PHYTAB format</description>
    <command interpreter="perl">
	#if $sp_opts.sp_opts_selector=="fasta"
		fasta2phytab.pl $infile 'from fasta' $partition $convert > $outfile
	#else
		fasta2phytab.pl $infile $sp_opts.species $partition $convert > $outfile
	#end if
    </command>
    <inputs>
	    <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
        <conditional name="sp_opts">
            <param name="sp_opts_selector" type="select" label="Species Name Source">
              <option value="fasta" selected="True">Take from fasta header</option>
              <option value="user">user input</option>
            </param>
            <when value="fasta">
	    <param name="species" type="hidden" value="from fasta" label="Species" help="" />
            </when>
            <when value="user">
		<param name="species" type="text" format="tabular" label="Input name of species" help="" />
            </when>
        </conditional>
	    <param name="partition" type="text" format="tabular" label="Name of partition" help="" />
       	    <param name="convert" type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Replace pipes with underscores' />
    </inputs>
    <outputs>
	<data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
    </outputs>
    <help>
**What it does**

FASTA2PHYTAB takes an input FASTA file with sequences from the same gene family, and adds species name - either from the fasta header or from a single text entry - and 
partition (gene family) name that will apply for all sequences. The output is a PHYTAB tabular format file.

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**Inputs**

A FASTA file with all sequences from the same gene family.

------

**Outputs**

PHYTAB file format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html

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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>