Mercurial > repos > greg > data_manager_vsnp_excel
changeset 2:79fcb638533e draft
Uploaded
author | greg |
---|---|
date | Mon, 10 Feb 2020 09:29:37 -0500 (2020-02-10) |
parents | d1bf63483e33 |
children | 4681f7129de9 |
files | data_manager/vsnp_excel_fetcher.xml |
diffstat | 1 files changed, 2 insertions(+), 18 deletions(-) [+] |
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--- a/data_manager/vsnp_excel_fetcher.xml Mon Feb 10 08:07:05 2020 -0500 +++ b/data_manager/vsnp_excel_fetcher.xml Mon Feb 10 09:29:37 2020 -0500 @@ -1,6 +1,6 @@ <?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> + <description>Download vSNP Excel files</description> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> @@ -26,89 +26,73 @@ </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 name fields +This tool fetches a vSNP Excel file associated with each supported genome reference to populate the vsnp_excel 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 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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 * **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 ]]></help> <citations>