Mercurial > repos > greg > data_manager_vsnp_excel

changeset 2:79fcb638533e draft

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Uploaded
author greg
date Mon, 10 Feb 2020 09:29:37 -0500
parents d1bf63483e33
children 4681f7129de9
files data_manager/vsnp_excel_fetcher.xml
diffstat 1 files changed, 2 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- 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>