Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

<tool id="get_1_gb" name="Get_1_GB" version="1.0">
    <description> Grab one sequence from GenBank using accession number query </description>
    <requirements>
        <requirement type="package">bioperl</requirement>
    </requirements>
    <command interpreter="perl">
        get_1_gb.pl $acc $database $outtype $outfile 2>&amp;1
    </command>
    <inputs>
	<param name="acc" type="text" label="Accession Number" />
        <param name="database" type="select" label="Protein or Nucleotide Data">
                <option value="nucleotide">Nucleotide</option>
                <option value="protein">Protein</option>
        </param>
        <param name="outtype" type="select" label="File Format">
                <option value="fasta">Fasta</option>
                <option value="genbank">GenBank</option>
        </param>
    </inputs>
    <outputs>
        <data format="txt" name="outfile" label="Sequence data from ${tool.name} with ${on_string}" />
    </outputs>
    <help>
**What it does**

Get_1_GB grabs one sequence from GenBank using accession number query.

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**Inputs**

GenBank accession number

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**Outputs**

FASTA or GenBank

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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

Additional Citations for this tool

Link to Genbank: http://www.ncbi.nlm.nih.gov/genbank/
    </help>
</tool>
author	osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date	Tue, 11 Mar 2014 12:19:13 -0700
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