Mercurial > repos > greg > data_manager_vsnp_excel

diff data_manager/vsnp_excel_fetcher.xml @ 1:d1bf63483e33 draft

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author greg
date Mon, 10 Feb 2020 08:07:05 -0500
parents 84a356e0950a
children 79fcb638533e
line wrap: on
line diff
--- a/data_manager/vsnp_excel_fetcher.xml	Fri Feb 07 13:02:25 2020 -0500
+++ b/data_manager/vsnp_excel_fetcher.xml	Mon Feb 10 08:07:05 2020 -0500
@@ -7,15 +7,16 @@
     <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'
+    --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="excel_url" type="text" value="" label="URL to download the Excel file associated with the selected FASTA reference" optional="False" />
+        <param name="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" />
@@ -25,7 +26,7 @@
         </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
+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
 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.
 
@@ -33,100 +34,83 @@
 
    * **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>
-