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comparison data_manager/vsnp_excel_fetcher.xml @ 2:79fcb638533e draft

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author greg
date Mon, 10 Feb 2020 09:29:37 -0500
parents d1bf63483e33
children 4681f7129de9
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1:d1bf63483e33 2:79fcb638533e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="vsnp_excel_fetcher" name="vSNP Excel data manager" tool_type="manage_data" profile="18.09" version="0.0.8"> 2 <tool id="vsnp_excel_fetcher" name="vSNP Excel data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
3 <description>Download reference databases</description> 3 <description>Download vSNP Excel files</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/vsnp_excel_fetcher.py' 8 python '$__tool_directory__/vsnp_excel_fetcher.py'
24 <tests> 24 <tests>
25 <test> 25 <test>
26 </test> 26 </test>
27 </tests> 27 </tests>
28 <help><![CDATA[ 28 <help><![CDATA[
29 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 29 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
30 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 30 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
31 at https://github.com/USDA-VS/vSNP_reference_options. 31 at https://github.com/USDA-VS/vSNP_reference_options.
32 32
33 * **Mycobacterium bovis AF2122/97** 33 * **Mycobacterium bovis AF2122/97**
34 34
35 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx 35 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx
36 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
37 36
38 * **Brucella abortus bv. 1 str. 9-941** 37 * **Brucella abortus bv. 1 str. 9-941**
39 38
40 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_define_filter.xlsx 39 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_define_filter.xlsx
41 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
42 40
43 * **Brucella abortus strain BER** 41 * **Brucella abortus strain BER**
44 42
45 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx 43 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx
46 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
47 44
48 * **Brucella canis ATCC 23365** 45 * **Brucella canis ATCC 23365**
49 46
50 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx 47 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx
51 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
52 48
53 * **Brucella ceti TE10759-12** 49 * **Brucella ceti TE10759-12**
54 50
55 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx 51 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx
56 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
57 52
58 * **Brucella melitensis bv. 1 str. 16M** 53 * **Brucella melitensis bv. 1 str. 16M**
59 54
60 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx 55 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx
61 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
62 56
63 * **Brucella melitensis bv. 3 str. Ether** 57 * **Brucella melitensis bv. 3 str. Ether**
64 58
65 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx 59 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx
66 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
67 60
68 * **Brucella melitensis BwIM_SOM_36b** 61 * **Brucella melitensis BwIM_SOM_36b**
69 62
70 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx 63 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx
71 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
72 64
73 * **Brucella melitensis ATCC 23457** 65 * **Brucella melitensis ATCC 23457**
74 66
75 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx 67 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx
76 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
77 68
78 * **Brucella ovis ATCC 25840** 69 * **Brucella ovis ATCC 25840**
79 70
80 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx 71 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx
81 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
82 72
83 * **Brucella suis 1330** 73 * **Brucella suis 1330**
84 74
85 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx 75 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx
86 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
87 76
88 * **Mycobacterium tuberculosis H37Rv** 77 * **Mycobacterium tuberculosis H37Rv**
89 78
90 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx 79 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx
91 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
92 80
93 * **Mycobacterium avium subsp. paratuberculosis strain Telford** 81 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
94 82
95 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx 83 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx
96 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
97 84
98 * **Mycobacterium avium subsp. paratuberculosis K-10** 85 * **Mycobacterium avium subsp. paratuberculosis K-10**
99 86
100 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx 87 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx
101 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
102 88
103 * **Brucella suis ATCC 23445** 89 * **Brucella suis ATCC 23445**
104 90
105 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx 91 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx
106 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
107 92
108 * **Brucella suis bv. 3 str. 686** 93 * **Brucella suis bv. 3 str. 686**
109 94
110 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx 95 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx
111 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
112 96
113 ]]></help> 97 ]]></help>
114 <citations> 98 <citations>
115 </citations> 99 </citations>
116 </tool> 100 </tool>