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comparison data_manager/vsnp_excel_fetcher.xml @ 0:84a356e0950a draft

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author greg
date Fri, 07 Feb 2020 13:02:25 -0500
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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">
3 <description>Download reference databases</description>
4 <requirements>
5 <requirement type="package" version="3.7">python</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/vsnp_excel_fetcher.py'
9 --dbkey '${all_fasta_source.fields.dbkey}'
10 --display_name '${all_fasta_source.fields.display_name}'
11 -excel_url '$excel_url'
12 ]]>
13 </command>
14 <inputs>
15 <param name="all_fasta_source" type="select" label="FASTA reference">
16 <options from_data_table="all_fasta"/>
17 </param>
18 <param name="excel_url" type="text" value="" label="URL to download the Excel file associated with the selected FASTA reference" optional="False" />
19 </inputs>
20 <outputs>
21 <data name="out_file" format="data_manager_json" />
22 </outputs>
23 <tests>
24 <test>
25 </test>
26 </tests>
27 <help><![CDATA[
28 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
29 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 at https://github.com/USDA-VS/vSNP_reference_options.
31
32 * **Mycobacterium bovis AF2122/97**
33
34 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx
35 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
36 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gff
37
38 * **Brucella abortus bv. 1 str. 9-941**
39
40 * **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 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gff
43
44 * **Brucella abortus strain BER**
45
46 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx
47 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
48 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gff
49
50 * **Brucella canis ATCC 23365**
51
52 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx
53 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
54 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gff
55
56 * **Brucella ceti TE10759-12**
57
58 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx
59 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
60 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gff
61
62 * **Brucella melitensis bv. 1 str. 16M**
63
64 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx
65 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
66 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gff
67
68 * **Brucella melitensis bv. 3 str. Ether**
69
70 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx
71 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
72 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gff
73
74 * **Brucella melitensis BwIM_SOM_36b**
75
76 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx
77 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
78 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gff
79
80 * **Brucella melitensis ATCC 23457**
81
82 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx
83 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
84 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gff
85
86 * **Brucella ovis ATCC 25840**
87
88 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx
89 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
90 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gff
91
92 * **Brucella suis 1330**
93
94 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx
95 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
96 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gff
97
98 * **Mycobacterium tuberculosis H37Rv**
99
100 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx
101 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
102 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gff
103
104 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
105
106 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx
107 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
108 * **Gff file**
109
110 * **Mycobacterium avium subsp. paratuberculosis K-10**
111
112 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx
113 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
114 * **Gff file**
115
116 * **Brucella suis ATCC 23445**
117
118 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx
119 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
120 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gff
121
122 * **Brucella suis bv. 3 str. 686**
123
124 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx
125 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
126 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gff
127
128 ]]></help>
129 <citations>
130 </citations>
131 </tool>
132