<tool id="phytab_ssr" name="phytab Similar Sequence Remover">
	<description>Removes redundant sequences</description>
        <requirements>
          <requirement type="package">java</requirement>
        </requirements>
	<command interpreter="python">phytab_ssr.py -i $in -s $percentage -a $h</command>

	<inputs>
		<param name="in" type="data" format="fasta,tabular,text" label="Input Sequences" help="Single/multi-gene PHYTAB or single-gene FASTA accepted." />
		<param name="percentage" type="float" value="0.99" label="Percentage similarity to be considered redundant."/>
		<param name="h" type="boolean" truevalue="t" falsevalue="f" label="Align first 100 characters instead of entire sequence" /> 
	</inputs>
	
	<outputs>
                <data from_work_dir="data/results.data" format="input" name="nonredundant seqs" label="${tool.name} on ${on_string}: Nonredundant Sequences"/>
	</outputs>
	
	<help>
**What it does**

phytab Similar Sequence Remover will take a set of sequences in either FASTA or phytab format and remove redundant sequences based on the minimum similarity percentage specified. 

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**Inputs**

FASTA, phytab

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**Outputs**

FASTA, phytab

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**Additional Information**

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

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>