Mercurial > repos > iuc > data_manager_bakta

annotate data_manager/bakta_build_database.xml @ 6:97b1b5ad1cda draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
author iuc
date Thu, 20 Jun 2024 19:13:58 +0000
parents baceff842902
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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1 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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2 <description>Bakta database builder</description>
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iuc
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3 <macros>
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iuc
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4 <import>macro.xml</import>
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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5 </macros>
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/bakta_build_database.py'
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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9 '$output_file'
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10 --database_version '$database_select'
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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11 $test_data_manager
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12 ]]></command>
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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13 <inputs>
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14 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
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15 <option value="5.1" selected="true">V5.1 (2024-01-19)</option>
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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16 <option value="5.1_light">V5.1 light (2024-01-19)</option>
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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17 <option value="5.0">V5.0 (2023-02-20)</option>
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18 <option value="5.0_light">V5.0 light (2023-02-20)</option>
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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19 <option value="4.0">V4.0 (2022-08-29)</option>
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20 <option value="3.1">V3.1 (2022-02-03)</option>
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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21 <option value="3.0">V3.0 (2021-08-05)</option>
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22 <option value="2.0">V2.0 (2021-04-05)</option>
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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23 <option value="1.1">V1.1 (2020-12-18)</option>
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24 <option value="1.0">V1.0 (2020-11-20)</option>
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25 </param>
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26 <param name="test_data_manager" type="hidden" value=""/>
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27 </inputs>
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28 <outputs>
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29 <data name="output_file" format="data_manager_json"/>
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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30 </outputs>
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31 <tests>
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32 <!-- Test 1 with version 1.0 -->
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33 <test expect_num_outputs="1">
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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34 <param name="test_data_manager" value="--test"/>
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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35 <param name="database_select" value="1.0"/>
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36 <output name="output_file" ftype="data_manager_json">
baceff842902 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e277883fca66013904bae930f04e7f3be5fcb1a2
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37 <assert_contents>
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38 <has_text text="data_tables"/>
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39 <has_text text="bakta_database"/>
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40 <has_text text="bakta_version"/>
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41 <has_text text="V1.0_2022-10-12"/>
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42 </assert_contents>
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43 </output>
0
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44 </test>
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45 <!-- Test 2 with the latest option -->
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46 <test expect_num_outputs="1">
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47 <param name="test_data_manager" value="--test"/>
5
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48 <param name="database_select" value="5.1_light"/>
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49 <output name="output_file" ftype="data_manager_json">
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50 <assert_contents>
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51 <has_text text="data_tables"/>
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52 <has_text text="bakta_database"/>
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53 <has_text text="bakta_version"/>
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54 <has_text text="V5.1light_2024-01-19"/>
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55 </assert_contents>
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56 </output>
3
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57 </test>
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58 <!-- Test 3 with light db -->
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59 <test expect_num_outputs="1">
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60 <param name="test_data_manager" value="--test"/>
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61 <param name="database_select" value="5.0_light"/>
5
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62 <output name="output_file" ftype="data_manager_json">
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63 <assert_contents>
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64 <has_text text="data_tables"/>
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65 <has_text text="bakta_database"/>
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66 <has_text text="bakta_version"/>
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67 <has_text text="V5.0light_2023-06-08"/>
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68 </assert_contents>
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69 </output>
0
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70 </test>
6
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71 <!-- Test 3 with light db -->
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72 <test expect_num_outputs="1">
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73 <param name="test_data_manager" value=""/>
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74 <param name="database_select" value="5.1_light"/>
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75 <output name="output_file" ftype="data_manager_json">
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76 <assert_contents>
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77 <has_text text="data_tables"/>
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78 <has_text text="bakta_database"/>
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79 <has_text text="bakta_version"/>
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80 <has_text text="V5.1light_2024-01-19"/>
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81 </assert_contents>
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82 </output>
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83 </test>
0
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84 </tests>
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85 <help><![CDATA[
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86 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
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87 ]]></help>
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88 <citations>
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89 <citation type="doi">10.1099/mgen.0.000685</citation>
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90 </citations>
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91 </tool>