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<tool id="remove_gbs_dupes" name="remove_gbs_dupes" version="1.0">
    <description> Finds duplicates in genbankstrip output files </description>
    <command interpreter="perl">
        remove_gbs_dupes.pl $infile $okfile $dupefile $subsp $var
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
        <param format="tabular" name="infile" type="data" label="Phytab Input file" help="Output of genbankstrip"/>
        <param name='subsp' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing subsp'/>
        <param name='var' type='boolean' checked='false' truevalue='1' falsevalue='0' label='Remove lines containing _var_'/>
    </inputs>
    <outputs>
	<data format="tabular" name="okfile" label="Unique phytab lines from ${on_string}" />
	<data format="tabular" name="dupefile" label="Duplicated phytab lines from ${on_string}" />
    </outputs>
    <help>
**What it does**

Finds species names that end in _2 or _3 or ... _N which are duplicate genes in a species in genbankstrip, and it writes those lines to another file.

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**Inputs**

1. PHYTAB format input file.

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**Outputs**

Two PHYTAB format files. One contains only unique species. The other contains duplicates. 

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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>