Mercurial > repos > iuc > data_manager_pangolin_data

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
author iuc
date Wed, 25 Sep 2024 15:42:43 +0000
parents 33158d21324d
children
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c22f6c820658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
iuc
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1 <tool id="data_manager_pangolin_data" name="pangolin-data data manager" version="0.0.1+galaxy1" tool_type="manage_data" profile="20.01">
c22f6c820658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
iuc
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2 <macros>
c22f6c820658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
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3 <import>macros.xml</import>
c22f6c820658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
iuc
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4 </macros>
0
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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5 <requirements>
1
c22f6c820658 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
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6 <requirement type="package" version="3.10">python</requirement>
0
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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7 <requirement type="package" version="22.1.2">pip</requirement>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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8 <requirement type="package" version="2.28.1">requests</requirement>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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9 <requirement type="package" version="2.37.1">git</requirement>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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10 <requirement type="package" version="3.2.0">git-lfs</requirement>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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11 <requirement type="package" version="3.1.27">gitpython</requirement>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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12 </requirements>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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13 <command detect_errors="exit_code"><![CDATA[
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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14 #set $dt_names = []
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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15 #if str($pangolin_data.enable) == "latest" or str($pangolin_data.enable) == "versions"
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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16 #set $dt_names = $dt_names + ["pangolin_data"]
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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17 #end if
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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18 #if str($pangolin_constellations.enable) == "latest" or str($pangolin_constellations.enable) == "versions"
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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19 #set $dt_names = $dt_names + ["pangolin_constellations"]
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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20 #end if
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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21 #if str($pangolin_assignment.enable) == "latest" or str($pangolin_assignment.enable) == "versions"
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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22 #set $dt_names = $dt_names + ["pangolin_assignment"]
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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23 #end if
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24 #for $dt_name in $dt_names
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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25 #set $data_table = $__app__.tool_data_tables.get($dt_name)
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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26 #if $data_table is not None and len($data_table.get_fields()) != 0
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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27 #set $known_revisions = '--known_revisions=' + ','.join([row[0] for row in $data_table.get_fields()])
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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28 #else
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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29 #set $known_revisions = ''
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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30 #end if
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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31 python '$__tool_directory__/pangolin_data_dm.py'
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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32 $known_revisions
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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33 #if $getVar($dt_name).enable == "latest"
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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34 --latest
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35 #else if $getVar($dt_name).enable == "versions"
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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36 --version_compatibility_file '$getVar($dt_name).compatibility_file'
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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37 --versions=$getVar($dt_name).versions
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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38 #end if
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39 '$dt_name'
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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40 datatable_cache.json
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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41 '${output_file}' &&
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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42 #end for
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43 cp datatable_cache.json '${output_file}'
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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44 ]]></command>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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45 <inputs>
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46 <expand macro="download_conditional" dt_name="pangolin_data" database_name="pangolin-data" software_name="pangolin" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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47 <expand macro="download_conditional" dt_name="pangolin_constellations" database_name="constellations" software_name="scorpio" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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48 <expand macro="download_conditional" dt_name="pangolin_assignment" database_name="pangolin-assignment" software_name="pangolin" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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49 </inputs>
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50 <outputs>
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51 <data name="output_file" format="data_manager_json"/>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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52 </outputs>
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53 <tests>
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54 <test expect_num_outputs="1">
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55 <conditional name="pangolin_data">
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56 <param name="enable" value="versions" />
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57 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
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58 <param name="versions" value="1.12" />
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59 </conditional>
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60 <conditional name="pangolin_constellations">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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61 <param name="enable" value="versions" />
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62 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
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63 <param name="versions" value="0.1.10" />
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64 </conditional>
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65 <conditional name="pangolin_assignment">
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66 <param name="enable" value="no" />
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67 </conditional>
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68 <output name="output_file">
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69 <assert_contents>
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70 <has_text text="pangolin-data v1.12" />
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71 <has_text text='"description": "constellations release v0.1.10"' />
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72 <has_text text='"min_scorpio_version": "0.3.17"' />
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73 <not_has_text text='"description": "pangolin-assignment' />
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74 </assert_contents>
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75 </output>
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76 </test>
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77 <test expect_num_outputs="1">
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78 <conditional name="pangolin_data">
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79 <param name="enable" value="no" />
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80 </conditional>
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81 <conditional name="pangolin_constellations">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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82 <param name="enable" value="no" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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83 </conditional>
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84 <conditional name="pangolin_assignment">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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85 <param name="enable" value="versions" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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86 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
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87 <param name="versions" value="1.12" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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88 </conditional>
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89 <output name="output_file">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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90 <assert_contents>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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91 <has_text text='"value": "v1.12"' />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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92 <has_text text='"min_pangolin_version": "4"' />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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93 <not_has_text text='"description": "constellations' />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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94 <not_has_text text='"description": "pangolin-data' />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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95 </assert_contents>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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96 </output>
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97 </test>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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98 <test expect_failure="true">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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99 <conditional name="pangolin_data">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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100 <param name="enable" value="no" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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101 </conditional>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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102 <conditional name="pangolin_constellations">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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103 <param name="enable" value="no" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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104 <param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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105 <param name="versions" value="0.0.40" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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106 </conditional>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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107 <conditional name="pangolin_assignment">
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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108 <param name="enable" value="no" />
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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109 </conditional>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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110 </test>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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111 </tests>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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112 <help><![CDATA[
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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113 This data managers fetches models (from the pangolin-data_,
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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114 pangolin-assignment_ and constellations_ repositories) for the
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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115 pangolin_ SARS-CoV-2 lineage typing tool and updates the pangolin_data,
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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116 pangolin_assignment and pangolin_constellations data tables.
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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117
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118 The default is to fetch the latest version of the databases. If specific versions of databases
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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119 need to be installed, a version compatibility matrix needs to be provided to help choose
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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120 the versions available. This matrix is stored in a CSV file in the pangolin repository
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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121 and can be downloaded at this link_. When loading this file into Galaxy, the csv datatype
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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122 needs to be selected, because the automatic format detection code detects this file as type txt.
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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123
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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124 **Note** that this data manager will only download database versions mentioned in the above
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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125 mentioned file. While effort is taken to ensure that this file is updated with each pangolin
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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126 database release, if that has not happened, the user of this data manager will need to provide
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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127 their own version compatibility matrix file in order to load the latest database release into Galaxy.
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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128
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129 The data manager will read the existing data tables and not re-download or replace databases
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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130 that are already present in those data tables.
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131
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132 .. _pangolin-data: https://github.com/cov-lineages/pangolin-data
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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133 .. _pangolin-assignment: https://github.com/cov-lineages/pangolin-assignment
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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134 .. _constellations: https://github.com/cov-lineages/constellations
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135 .. _pangolin: https://github.com/cov-lineages/pangolin
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136 .. _link: https://raw.githubusercontent.com/cov-lineages/pangolin/master/pangolin/data/data_compatibility.csv
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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137 ]]></help>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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138 <citations>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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139 <citation type="doi">10.1093/ve/veab064</citation>
33158d21324d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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140 </citations>
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141 </tool>