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1 <?xml version="1.0"?>
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2 <tool id="vsnp_excel_fetcher" name="vSNP Excel data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
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3 <description>Download reference databases</description>
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4 <requirements>
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5 <requirement type="package" version="3.7">python</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/vsnp_excel_fetcher.py'
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9 --dbkey '${all_fasta_source.fields.dbkey}'
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10 --display_name '${all_fasta_source.fields.display_name}'
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11 -excel_url '$excel_url'
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="all_fasta_source" type="select" label="FASTA reference">
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16 <options from_data_table="all_fasta"/>
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17 </param>
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18 <param name="excel_url" type="text" value="" label="URL to download the Excel file associated with the selected FASTA reference" optional="False" />
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19 </inputs>
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20 <outputs>
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21 <data name="out_file" format="data_manager_json" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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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
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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
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30 at https://github.com/USDA-VS/vSNP_reference_options.
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31
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32 * **Mycobacterium bovis AF2122/97**
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33
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34 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_define_filter.xlsx
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35 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
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36 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gff
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37
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38 * **Brucella abortus bv. 1 str. 9-941**
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39
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40 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_define_filter.xlsx
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41 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
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42 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gff
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43
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44 * **Brucella abortus strain BER**
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45
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46 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_define_filter.xlsx
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47 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
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48 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gff
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49
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50 * **Brucella canis ATCC 23365**
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51
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52 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_define_filter.xlsx
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53 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
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54 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gff
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55
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56 * **Brucella ceti TE10759-12**
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57
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58 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_define_filter.xlsx
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59 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
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60 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gff
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61
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62 * **Brucella melitensis bv. 1 str. 16M**
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63
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64 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_define_filter.xlsx
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65 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
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66 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gff
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67
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68 * **Brucella melitensis bv. 3 str. Ether**
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69
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70 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_define_filter.xlsx
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71 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
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72 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gff
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73
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74 * **Brucella melitensis BwIM_SOM_36b**
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75
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76 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_define_filter.xlsx
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77 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
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78 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gff
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79
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80 * **Brucella melitensis ATCC 23457**
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81
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82 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_define_filter.xlsx
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83 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
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84 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gff
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85
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86 * **Brucella ovis ATCC 25840**
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87
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88 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_define_filter.xlsx
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89 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
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90 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gff
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91
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92 * **Brucella suis 1330**
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93
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94 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_define_filter.xlsx
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95 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
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96 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gff
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97
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98 * **Mycobacterium tuberculosis H37Rv**
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99
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100 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_define_filter.xlsx
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101 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
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102 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gff
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103
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104 * **Mycobacterium avium subsp. paratuberculosis strain Telford**
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105
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106 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_define_filter.xlsx
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107 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
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108 * **Gff file**
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109
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110 * **Mycobacterium avium subsp. paratuberculosis K-10**
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111
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112 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_define_filter.xlsx
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113 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
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114 * **Gff file**
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115
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116 * **Brucella suis ATCC 23445**
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117
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118 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_define_filter.xlsx
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119 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
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120 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gff
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121
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122 * **Brucella suis bv. 3 str. 686**
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123
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124 * **Excel file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_define_filter.xlsx
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125 * **Genbank file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
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126 * **Gff file** https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gff
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127
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128 ]]></help>
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129 <citations>
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130 </citations>
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131 </tool>
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132
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