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comparison data_manager/vsnp_genbank_fetcher.xml @ 0:efed56c325da draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_genbank commit 31f4453e44da62788efd01736ed57ad483383b09"
author iuc
date Sat, 09 May 2020 17:27:45 -0400
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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 <param name="all_fasta_source" value="AF2122"/>
27 <param name="url" value="https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk"/>
28 <output name="out_file" value="vsnp_genbank.json" compare="contains"/>
29 </test>
30 </tests>
31 <help><![CDATA[
32 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
33 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
34 at https://github.com/USDA-VS/vSNP_reference_options.
35
36 * **Mycobacterium bovis AF2122/97**
37
38 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
39
40 * **Brucella abortus bv. 1 str. 9-941**
41
42 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
43
44 * **Brucella abortus strain BER**
45
46 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
47
48 * **Brucella canis ATCC 23365**
49
50 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
51
52 * **Brucella ceti TE10759-12**
53
54 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
55
56 * **Brucella melitensis bv. 1 str. 16M**
57
58 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
59
60 * **Brucella melitensis bv. 3 str. Ether**
61
62 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
63
64 * **Brucella melitensis BwIM_SOM_36b**
65
66 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
67
68 * **Brucella melitensis ATCC 23457**
69
70 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
71
72 * **Brucella ovis ATCC 25840**
73
74 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
75
76 * **Brucella suis 1330**
77
78 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
79
80 * **Mycobacterium tuberculosis H37Rv**
81
82 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
83
84 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
85
86 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
87
88 * **Mycobacterium avium subsp. paratuberculosis K-10**
89
90 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
91
92 * **Brucella suis ATCC 23445**
93
94 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
95
96 * **Brucella suis bv. 3 str. 686**
97
98 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
99
100 ]]></help>
101 <citations>
102 </citations>
103 </tool>