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comparison data_manager/vsnp_excel_fetcher.xml @ 1:54389d791983 draft

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author greg
date Mon, 10 Feb 2020 13:06:19 +0000
parents f7183dcf0430
children 089ee96573aa
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0:f7183dcf0430 1:54389d791983
5 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/vsnp_excel_fetcher.py' 8 python '$__tool_directory__/vsnp_excel_fetcher.py'
9 --dbkey '${all_fasta_source.fields.dbkey}' 9 --dbkey '${all_fasta_source.fields.dbkey}'
10 --display_name '${all_fasta_source.fields.display_name}' 10 --name '${all_fasta_source.fields.name}'
11 -excel_url '$excel_url' 11 --out_file '$out_file'
12 --url '$url'
12 ]]> 13 ]]>
13 </command> 14 </command>
14 <inputs> 15 <inputs>
15 <param name="all_fasta_source" type="select" label="FASTA reference"> 16 <param name="all_fasta_source" type="select" label="FASTA reference">
16 <options from_data_table="all_fasta"/> 17 <options from_data_table="all_fasta"/>
17 </param> 18 </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 <param name="url" type="text" value="" label="URL to download the Excel file associated with the selected FASTA reference" optional="False" />
19 </inputs> 20 </inputs>
20 <outputs> 21 <outputs>
21 <data name="out_file" format="data_manager_json" /> 22 <data name="out_file" format="data_manager_json" />
22 </outputs> 23 </outputs>
23 <tests> 24 <tests>
24 <test> 25 <test>
25 </test> 26 </test>
26 </tests> 27 </tests>
27 <help><![CDATA[ 28 <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 This tool fetches a vSNP Excel file associated with each supported genome reference to populate the vsnp_ecxel data table. The dbkey and 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 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 at https://github.com/USDA-VS/vSNP_reference_options.
31 32
32 * **Mycobacterium bovis AF2122/97** 33 * **Mycobacterium bovis AF2122/97**
33 34
34 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx 35 * **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 * **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 37
38 * **Brucella abortus bv. 1 str. 9-941** 38 * **Brucella abortus bv. 1 str. 9-941**
39 39
40 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_define_filter.xlsx 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 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 42
44 * **Brucella abortus strain BER** 43 * **Brucella abortus strain BER**
45 44
46 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx 45 * **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 46 * **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 47
50 * **Brucella canis ATCC 23365** 48 * **Brucella canis ATCC 23365**
51 49
52 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx 50 * **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 51 * **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 52
56 * **Brucella ceti TE10759-12** 53 * **Brucella ceti TE10759-12**
57 54
58 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx 55 * **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 56 * **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 57
62 * **Brucella melitensis bv. 1 str. 16M** 58 * **Brucella melitensis bv. 1 str. 16M**
63 59
64 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx 60 * **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 61 * **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 62
68 * **Brucella melitensis bv. 3 str. Ether** 63 * **Brucella melitensis bv. 3 str. Ether**
69 64
70 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx 65 * **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 66 * **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 67
74 * **Brucella melitensis BwIM_SOM_36b** 68 * **Brucella melitensis BwIM_SOM_36b**
75 69
76 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx 70 * **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 71 * **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 72
80 * **Brucella melitensis ATCC 23457** 73 * **Brucella melitensis ATCC 23457**
81 74
82 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx 75 * **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 76 * **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 77
86 * **Brucella ovis ATCC 25840** 78 * **Brucella ovis ATCC 25840**
87 79
88 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx 80 * **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 81 * **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 82
92 * **Brucella suis 1330** 83 * **Brucella suis 1330**
93 84
94 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx 85 * **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 86 * **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 87
98 * **Mycobacterium tuberculosis H37Rv** 88 * **Mycobacterium tuberculosis H37Rv**
99 89
100 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx 90 * **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 91 * **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 92
104 * **Mycobacterium avium subsp. paratuberculosis strain Telford** 93 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
105 94
106 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx 95 * **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 96 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
108 * **Gff file**
109 97
110 * **Mycobacterium avium subsp. paratuberculosis K-10** 98 * **Mycobacterium avium subsp. paratuberculosis K-10**
111 99
112 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx 100 * **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 101 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
114 * **Gff file**
115 102
116 * **Brucella suis ATCC 23445** 103 * **Brucella suis ATCC 23445**
117 104
118 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx 105 * **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 106 * **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
121 107
122 * **Brucella suis bv. 3 str. 686** 108 * **Brucella suis bv. 3 str. 686**
123 109
124 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx 110 * **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 111 * **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
127 112
128 ]]></help> 113 ]]></help>
129 <citations> 114 <citations>
130 </citations> 115 </citations>
131 </tool> 116 </tool>
132