|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool id="vsnp_dnaprints_fetcher" name="vSNP DNAprints data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
|
|
|
3 <description>Download vSNP DNAprints files</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="3.7">python</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command detect_errors="exit_code"><![CDATA[
|
|
|
8 python '$__tool_directory__/vsnp_dnaprints_fetcher.py'
|
|
|
9 --dbkey '${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>
|
|
1
|
19 <param name="url" type="text" value="" label="URL to download the DNAprints file associated with the selected FASTA reference" optional="False"/>
|
|
0
|
20 </inputs>
|
|
|
21 <outputs>
|
|
1
|
22 <data name="out_file" format="data_manager_json"/>
|
|
0
|
23 </outputs>
|
|
|
24 <tests>
|
|
|
25 <test>
|
|
1
|
26 <param name="all_fasta_source" value="AF2122"/>
|
|
|
27 <param name="url" value="https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Mycobacterium_AF2122/NC_002945v4.yml"/>
|
|
|
28 <output name="out_file" value="vsnp_dnaprints.json" compare="contains"/>
|
|
0
|
29 </test>
|
|
|
30 </tests>
|
|
|
31 <help><![CDATA[
|
|
|
32 This tool fetches a vSNP DNAprints file associated with each supported genome reference to populate the vsnp_dnaprints data table. The dbkey and name fields
|
|
|
33 in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary. These public vSNP DNAprints files are available in GitHub
|
|
|
34 at https://github.com/USDA-VS/vSNP_reference_options.
|
|
|
35
|
|
|
36 * **Mycobacterium bovis AF2122/97**
|
|
|
37
|
|
|
38 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Mycobacterium_AF2122/NC_002945v4.yml
|
|
|
39
|
|
|
40 * **Brucella abortus bv. 1 str. 9-941**
|
|
|
41
|
|
|
42 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_abortus1/NC_006932-NC_006933.yml
|
|
|
43
|
|
|
44 * **Brucella abortus strain BER**
|
|
|
45
|
|
|
46 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.yml
|
|
|
47
|
|
|
48 * **Brucella canis ATCC 23365**
|
|
|
49
|
|
|
50 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_canis/NC_010103-NC_010104.yml
|
|
|
51
|
|
|
52 * **Brucella ceti TE10759-12**
|
|
|
53
|
|
|
54 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_ceti2/NC_022905-NC_022906.yml
|
|
|
55
|
|
|
56 * **Brucella melitensis bv. 1 str. 16M**
|
|
|
57
|
|
|
58 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_melitensis-bv1/NC_003317-NC_003318.yml
|
|
|
59
|
|
|
60 * **Brucella melitensis bv. 3 str. Ether**
|
|
|
61
|
|
|
62 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.yml
|
|
|
63
|
|
|
64 * **Brucella melitensis BwIM_SOM_36b**
|
|
|
65
|
|
|
66 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.yml
|
|
|
67
|
|
|
68 * **Brucella melitensis ATCC 23457**
|
|
|
69
|
|
|
70 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_melitensis-bv2/NC_012441-NC_012442.yml
|
|
|
71
|
|
|
72 * **Brucella ovis ATCC 25840**
|
|
|
73
|
|
|
74 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_ovis/NC_009505-NC_009504.yml
|
|
|
75
|
|
|
76 * **Brucella suis 1330**
|
|
|
77
|
|
|
78 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_suis1/NC_017251-NC_017250.yml
|
|
|
79
|
|
|
80 * **Mycobacterium tuberculosis H37Rv**
|
|
|
81
|
|
|
82 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Mycobacterium_H37/NC_000962.yml
|
|
|
83
|
|
|
84 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
|
|
|
85
|
|
|
86 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/para-CP033688/CP033688.yml
|
|
|
87
|
|
|
88 * **Mycobacterium avium subsp. paratuberculosis K-10**
|
|
|
89
|
|
|
90 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/para-NC002944/NC_002944.yml
|
|
|
91
|
|
|
92 * **Brucella suis ATCC 23445**
|
|
|
93
|
|
|
94 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_suis2/NC_010169-NC_010167.yml
|
|
|
95
|
|
|
96 * **Brucella suis bv. 3 str. 686**
|
|
|
97
|
|
|
98 * **DNAprints file** https://raw.githubusercontent.com/USDA-VS/vSNP_reference_options/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.yml
|
|
|
99
|
|
|
100 ]]></help>
|
|
|
101 <citations>
|
|
|
102 </citations>
|
|
|
103 </tool>
|
