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author greg
date Fri, 07 Feb 2020 13:02:25 -0500
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<?xml version="1.0"?>
<tool id="vsnp_excel_fetcher" name="vSNP Excel data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
    <description>Download reference databases</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/vsnp_excel_fetcher.py'
    --dbkey '${all_fasta_source.fields.dbkey}'
    --display_name '${all_fasta_source.fields.display_name}'
    -excel_url '$excel_url'
    ]]>
    </command>
    <inputs>
        <param name="all_fasta_source" type="select" label="FASTA reference">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="excel_url" type="text" value="" label="URL to download the Excel file associated with the selected FASTA reference" optional="False" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
This tool fetches a vSNP Excel file associated with each supported genome reference to populate the vsnp_ecxel data table.  The dbkey and display_name fields
in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary.  These public vSNP Excel files are available in GitHub
at https://github.com/USDA-VS/vSNP_reference_options.

 * **Mycobacterium bovis AF2122/97**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gff

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gff

 * **Brucella abortus strain BER**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gff

 * **Brucella canis ATCC 23365**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gff

 * **Brucella ceti TE10759-12**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gff

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gff

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gff

 * **Brucella melitensis BwIM_SOM_36b**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gff

 * **Brucella melitensis ATCC 23457**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gff

 * **Brucella ovis ATCC 25840**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gff

 * **Brucella suis 1330**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gff

 * **Mycobacterium tuberculosis H37Rv**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gff

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
   * **Gff file**      

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
   * **Gff file**      

 * **Brucella suis ATCC 23445**

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gff

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

   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx
   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
   * **Gff file**      https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gff

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