Mercurial > repos > greg > vsnp_excel_filter
comparison data_manager/vsnp_excel_filter_fetcher.xml @ 0:3fbd172e4055 draft default tip
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author | greg |
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date | Mon, 09 Mar 2020 13:42:19 -0400 |
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-1:000000000000 | 0:3fbd172e4055 |
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1 <?xml version="1.0"?> | |
2 <tool id="vsnp_excel_filter_fetcher" name="vSNP Excel Filter data manager" tool_type="manage_data" profile="18.09" version="0.0.8"> | |
3 <description>Download vSNP Excel files</description> | |
4 <requirements> | |
5 <requirement type="package" version="3.7">python</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 python '$__tool_directory__/vsnp_excel_filter_fetcher.py' | |
9 --dbkey '${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 Excel Filter 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 Excel Filter file associated with each supported genome reference to populate the vsnp_excel_filter data table. | |
30 The dbkey and name fields in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary. These | |
31 public vSNP Excel Filter files are available in GitHub at https://github.com/USDA-VS/vSNP_reference_options. Note that the file names | |
32 are a bit confusing. This tool must be used for Excel files with the pattern "remove_from_analysis" in the name. | |
33 | |
34 * **Mycobacterium bovis AF2122/97** | |
35 | |
36 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_remove_from_analysis.xlsx | |
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_remove_from_analysis.xlsx | |
41 | |
42 * **Brucella abortus strain BER** | |
43 | |
44 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_remove_from_analysis.xlsx | |
45 | |
46 * **Brucella canis ATCC 23365** | |
47 | |
48 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_remove_from_analysis.xlsx | |
49 | |
50 * **Brucella ceti TE10759-12** | |
51 | |
52 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_remove_from_analysis.xlsx | |
53 | |
54 * **Brucella melitensis bv. 1 str. 16M** | |
55 | |
56 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_remove_from_analysis.xlsx | |
57 | |
58 * **Brucella melitensis bv. 3 str. Ether** | |
59 | |
60 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_remove_from_analysis.xlsx | |
61 | |
62 * **Brucella melitensis BwIM_SOM_36b** | |
63 | |
64 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_remove_from_analysis.xlsx | |
65 | |
66 * **Brucella melitensis ATCC 23457** | |
67 | |
68 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_remove_from_analysis.xlsx | |
69 | |
70 * **Brucella ovis ATCC 25840** | |
71 | |
72 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_remove_from_analysis.xlsx | |
73 | |
74 * **Brucella suis 1330** | |
75 | |
76 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_remove_from_analysis.xlsx | |
77 | |
78 * **Mycobacterium tuberculosis H37Rv** | |
79 | |
80 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_remove_from_analysis.xlsx | |
81 | |
82 * **Mycobacterium avium subsp. paratuberculosis strain Telford** | |
83 | |
84 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_remove_from_analysis.xlsx | |
85 | |
86 * **Mycobacterium avium subsp. paratuberculosis K-10** | |
87 | |
88 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_remove_from_analysis.xlsx | |
89 | |
90 * **Brucella suis ATCC 23445** | |
91 | |
92 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_remove_from_analysis.xlsx | |
93 | |
94 * **Brucella suis bv. 3 str. 686** | |
95 | |
96 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_remove_from_analysis.xlsx | |
97 | |
98 ]]></help> | |
99 <citations> | |
100 </citations> | |
101 </tool> |