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<tool id="genbankstrip" name="GenBank_strip" version="1.0.0">
    <description> Extracts sequences from GenBank files by gene name </description>
    <command interpreter="perl">
	genbankstrip.pl "-f"$data_file "-g"$gene "-l"$length $sp -op 
    </command>
    <inputs>
        <param format="txt" name="data_file" type="data" optional="false" label="GenBank flat file"/>
	<param name="gene" type="text" label="Gene to extract" help="Name must match the GenBank files or be synonymized" />
	<param name="length" type="integer" value="75" label="Minimum gene length" help="Does not retain short genes." />
	<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="tabular" name="stripfile" label="Summary ${tool.name} with ${on_string}" from_work_dir="striplist.txt"/>
        <data format="tabular" name="phytabfile" label="Phytab Data ${tool.name} with ${on_string}" from_work_dir="osiris_gbs.phytab"/>
    </outputs>
    <help>
**What it does**

Extracts sequences from GenBank flat file based on gene name.

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**Inputs**

There are two alternative ways to input information.
1. A list of Accession numbers in a text file that is uploaded to the Galaxy history.
2. Optionally, the user can paste in a list of accession numbers separated by spaces.

------

**Outputs**

The user selects which output format to use for data downloaded from GenBank. Options Include::
  1. GenBank format
  2. FASTA format
  3. phytab format 

phytab format includes a gene name, which is not standardized in GenBank format, so the user must add manually the gene 
family names for all entries. If adding only one gene name, that will be used for all entries.

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**Additional Information**

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

Please direct questions or comments to [e-mail] 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>