<tool id="gb_gene_summary" name="GB_gene_summary" version="1.0.0">
    <description>Summarizes gene names in a GenBank flatfile</description>
    <command interpreter="perl">
	genbankstrip.pl "-f"$data_file "-l"$length "-ts"$species $sp > $logfile
    </command>
    <inputs>
        <param format="txt" name="data_file" type="data" optional="false" label="GenBank flat file"/>
	<param name="length" type="integer" value="75" label="Minimum gene length" help="Does not retain short genes." />
	<param name="species" type="integer" value="5" label="Minimum" help="Only shows genes present in >x species." />
	<param name='sp' type='boolean' checked='true' truevalue='-s' falsevalue='' label='Ignore undefined species' help='For example Vargula sp. would be ignored' />
    </inputs>
    <outputs>
        <data format="txt" name="logfile" label="Screen output from ${tool.name} with ${on_string}" />
        <data format="tabular" name="stripfile" label="Summary ${tool.name} with ${on_string}" from_work_dir="striplist.txt"/>
    </outputs>
    <help>
**What it does**

Summarizes gene names in a genbank flatfile.

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**Inputs**

A genbank flatfile.

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**Outputs**

A summary of gene names, and how many species are have data available for each gene.

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**Additional Information**

The gene names can be used to pull genes using genbankstrip.
Often, the same gene will have many names in genbank. These names can be synonymized by altering the genbankstrip.pl script.

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>