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comparison data_manager/vsnp_genbank_fetcher.xml @ 0:f1a7a3faaf3d draft

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author greg
date Mon, 10 Feb 2020 09:36:20 -0500
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1 <?xml version="1.0"?>
2 <tool id="vsnp_genbank_fetcher" name="vSNP Genbank data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
3 <description>Download vSNP Genbank files</description>
4 <requirements>
5 <requirement type="package" version="3.7">python</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/vsnp_genbank_fetcher.py'
9 --dbkey '${all_fasta_source.fields.dbkey}'
10 --name '${all_fasta_source.fields.name}'
11 --out_file '$out_file'
12 --url '$url'
13 ]]>
14 </command>
15 <inputs>
16 <param name="all_fasta_source" type="select" label="FASTA reference">
17 <options from_data_table="all_fasta"/>
18 </param>
19 <param name="url" type="text" value="" label="URL to download the Genbank file associated with the selected FASTA reference" optional="False" />
20 </inputs>
21 <outputs>
22 <data name="out_file" format="data_manager_json" />
23 </outputs>
24 <tests>
25 <test>
26 </test>
27 </tests>
28 <help><![CDATA[
29 This tool fetches a vSNP Genbank file associated with each supported genome reference to populate the vsnp_genbank 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 Genbank files are available in GitHub
31 at https://github.com/USDA-VS/vSNP_reference_options.
32
33 * **Mycobacterium bovis AF2122/97**
34
35 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
36
37 * **Brucella abortus bv. 1 str. 9-941**
38
39 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
40
41 * **Brucella abortus strain BER**
42
43 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
44
45 * **Brucella canis ATCC 23365**
46
47 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
48
49 * **Brucella ceti TE10759-12**
50
51 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
52
53 * **Brucella melitensis bv. 1 str. 16M**
54
55 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
56
57 * **Brucella melitensis bv. 3 str. Ether**
58
59 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
60
61 * **Brucella melitensis BwIM_SOM_36b**
62
63 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
64
65 * **Brucella melitensis ATCC 23457**
66
67 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
68
69 * **Brucella ovis ATCC 25840**
70
71 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
72
73 * **Brucella suis 1330**
74
75 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
76
77 * **Mycobacterium tuberculosis H37Rv**
78
79 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
80
81 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
82
83 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
84
85 * **Mycobacterium avium subsp. paratuberculosis K-10**
86
87 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
88
89 * **Brucella suis ATCC 23445**
90
91 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
92
93 * **Brucella suis bv. 3 str. 686**
94
95 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
96
97 ]]></help>
98 <citations>
99 </citations>
100 </tool>