<?xml version="1.0"?>
<tool id="vsnp_genbank_fetcher" name="vSNP Genbank data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
    <description>Download vSNP Genbank files</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/vsnp_genbank_fetcher.py'
    --dbkey '${all_fasta_source.fields.dbkey}'
    --name '${all_fasta_source.fields.name}'
    --out_file '$out_file'
    --url '$url'
    ]]>
    </command>
    <inputs>
        <param name="all_fasta_source" type="select" label="FASTA reference">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="url" type="text" value="" label="URL to download the Genbank file associated with the selected FASTA reference" optional="False" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="AF2122"/>
            <param name="url" value="https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk"/>
            <output name="out_file" value="vsnp_genbank.json" compare="contains"/>
        </test>
    </tests>
    <help><![CDATA[
This tool fetches a vSNP Genbank file associated with each supported genome reference to populate the vsnp_genbank data table.  The dbkey and name fields
in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary.  These public vSNP Genbank files are available in GitHub
at https://github.com/USDA-VS/vSNP_reference_options.

 * **Mycobacterium bovis AF2122/97**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk

 * **Brucella abortus bv. 1 str. 9-941**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk

 * **Brucella abortus strain BER**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk

 * **Brucella canis ATCC 23365**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk

 * **Brucella ceti TE10759-12**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk

 * **Brucella melitensis bv. 1 str. 16M**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk

 * **Brucella melitensis bv. 3 str. Ether**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk

 * **Brucella melitensis BwIM_SOM_36b**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk

 * **Brucella melitensis ATCC 23457**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk

 * **Brucella ovis ATCC 25840**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk

 * **Brucella suis 1330**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk

 * **Mycobacterium tuberculosis H37Rv**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk

 * **Mycobacterium avium subsp. paratuberculosis strain Telford**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk

 * **Mycobacterium avium subsp. paratuberculosis K-10**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk

 * **Brucella suis ATCC 23445**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk

 * **Brucella suis bv. 3 str. 686**

   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk

    ]]></help>
    <citations>
    </citations>
</tool>