comparison getdata/get_gb_sp.xml @ 0:5b9a38ec4a39 draft default tip

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0:5b9a38ec4a39

<tool id="get_gb_sp" name="Get_GB_sp" version="1.0">
    <description> Grab All GenBank Data from a text list of species </description>
    <requirements>
         <requirement type="perl-module">Bio</requirement>
    </requirements>
    <command interpreter="perl">
	        get_gb_sp.pl $data_file $database $outtype $outfile $nffile 2> error.log
    </command>
    <inputs>
        <param format="txt" name="data_file" type="data" optional="false" label="Text list of species" help="One species per line"/>

        <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="Output File Format">
                <option value="fasta">Fasta</option>
                <option value="genbank">GenBank</option>
            </param>
    </inputs>
    <outputs>
        <data format="txt" name="nffile" label="No genbank data ${tool.name} with ${on_string}" />
        <data format="txt" name="outfile" label="Sequence Data from ${tool.name} with ${on_string}" />
    </outputs>
    <help>
**What it does**

Downloads ALL data from GenBank based on species names.

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**Inputs**

A text list of species names (or genus names will retrieve all data for a genus.)

------

**Outputs**

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

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**Additional Information**

GenBank format can be converted to phytab or other formats using GenBankstrip.

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>