<tool id="get_gb" name="Get_GB" version="1.0">
    <description> Grab GenBank Data from a text list of accession numbers </description>
    <requirements>
         <requirement type="perl-module">Bio</requirement>
    </requirements>
    <command interpreter="perl">
	#if $outtypeconditional.outtype == "phytab":
	        get_gb.pl $data_file $database $outtypeconditional.outtype $outfile '$manual' '$mannames' '$outtypeconditional.genenames'
	#else:
	        get_gb.pl $data_file $database $outtypeconditional.outtype $outfile '$manual' '$mannames' None
	#end if
    </command>
    <inputs>
        <param format="txt" name="data_file" type="data" optional="true" label="Text list of accession numbers" help="One Accession number per line"/>
	<param name="manual" type="text" label="Paste in accession numbers (optional)" help="You can optionally list the Accession numbers here (spaces between) The name of one, which will ignore the text list above"/>
	<param name="mannames" type="text" label="Paste in new names for sequences (optional)" help="You can optionally list Custom Names (with spaces between) for the sequences in the same order as the Accession Numbers"/>

        <param name="database" type="select" label="Protein or Nucleotide Data">
                <option value="nucleotide">Nucleotide</option>
                <option value="protein">Protein</option>
        </param>

        <conditional name="outtypeconditional">
            <param name="outtype" type="select" label="Output File Format">
                <option value="fasta">Fasta</option>
                <option value="genbank">GenBank</option>
                <option value="phytab">phytab</option>
            </param>
            <when value="phytab">
                <param name="genenames" type="text" label="Gene Names (C3) for phytab format" />
            </when>
        </conditional>


    </inputs>
    <outputs>
        <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" />
    </outputs>
    <help>
**What it does**

Downloads data from GenBank based on Accession numbers.

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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.

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**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 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>