Mercurial > repos > iuc > data_manager_bakta

comparison data_manager/bakta_build_database.xml @ 5:ba7b35caf55c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 19:13:47 +0000
parents c0bd27c2bc9b
children
comparison
equal deleted inserted replaced
4:b71b550553b2 5:ba7b35caf55c
2 <description>Bakta database builder</description> 2 <description>Bakta database builder</description>
3 <macros> 3 <macros>
4 <import>macro.xml</import> 4 <import>macro.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 python '$__tool_directory__/bakta_build_database.py'
9 python '$__tool_directory__/bakta_build_database.py' 9 '$output_file'
10 '$output_file' 10 --database_version '$database_select'
11 --database_version '$database_select' 11 $test_data_manager
12 $test_data_manager 12 ]]></command>
13 ]]></command>
14 <inputs> 13 <inputs>
15 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> 14 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
16 <option value="latest" selected="true">Latest available version</option> 15 <option value="5.1" selected="true">V5.1 (2024-01-19)</option>
17 <option value="1.0">V1.0_2020-11-20</option> 16 <option value="5.1_light">V5.1 light (2024-01-19)</option>
18 <option value="1.1">V1.1_2020-12-18</option> 17 <option value="5.0">V5.0 (2023-02-20)</option>
19 <option value="2.0">V2.0_2021-04-05</option> 18 <option value="5.0_light">V5.0 light (2023-02-20)</option>
20 <option value="3.0">V3.0_2021-08-05</option> 19 <option value="4.0">V4.0 (2022-08-29)</option>
21 <option value="3.1">V3.1_2022-02-03</option> 20 <option value="3.1">V3.1 (2022-02-03)</option>
22 <option value="4.0">V4.0_2022-08-29</option> 21 <option value="3.0">V3.0 (2021-08-05)</option>
23 <option value="5.0">V5.0_2023-02-20</option> 22 <option value="2.0">V2.0 (2021-04-05)</option>
24 <option value="5.0_light">V5.0_light_2023-02-20</option> 23 <option value="1.1">V1.1 (2020-12-18)</option>
24 <option value="1.0">V1.0 (2020-11-20)</option>
25 </param> 25 </param>
26 <param name="test_data_manager" type="hidden" value=""/> 26 <param name="test_data_manager" type="hidden" value=""/>
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="output_file" format="data_manager_json"/> 29 <data name="output_file" format="data_manager_json"/>
31 <tests> 31 <tests>
32 <!-- Test 1 with version 1.0 --> 32 <!-- Test 1 with version 1.0 -->
33 <test expect_num_outputs="1"> 33 <test expect_num_outputs="1">
34 <param name="test_data_manager" value="--test"/> 34 <param name="test_data_manager" value="--test"/>
35 <param name="database_select" value="1.0"/> 35 <param name="database_select" value="1.0"/>
36 <output name="output_file" value="bakta_test_data_manager1.json" /> 36 <output name="output_file" ftype="data_manager_json">
37 <assert_contents>
38 <has_text text="data_tables"/>
39 <has_text text="bakta_database"/>
40 <has_text text="bakta_version"/>
41 <has_text text="V1.0_2022-10-12"/>
42 </assert_contents>
43 </output>
37 </test> 44 </test>
38 <!-- Test 2 with the latest option --> 45 <!-- Test 2 with the latest option -->
39 <test expect_num_outputs="1"> 46 <test expect_num_outputs="1">
40 <param name="test_data_manager" value="--test"/> 47 <param name="test_data_manager" value="--test"/>
41 <param name="database_select" value="latest"/> 48 <param name="database_select" value="5.1_light"/>
42 <output name="output_file" value="bakta_test_data_manager2.json" /> 49 <output name="output_file" ftype="data_manager_json">
50 <assert_contents>
51 <has_text text="data_tables"/>
52 <has_text text="bakta_database"/>
53 <has_text text="bakta_version"/>
54 <has_text text="V5.1light_2024-01-19"/>
55 </assert_contents>
56 </output>
43 </test> 57 </test>
44 <!-- Test 3 with light db --> 58 <!-- Test 3 with light db -->
45 <test expect_num_outputs="1"> 59 <test expect_num_outputs="1">
46 <param name="test_data_manager" value="--test"/> 60 <param name="test_data_manager" value="--test"/>
47 <param name="database_select" value="5.0_light"/> 61 <param name="database_select" value="5.0_light"/>
48 <output name="output_file" value="bakta_test_data_manager3.json" /> 62 <output name="output_file" ftype="data_manager_json">
63 <assert_contents>
64 <has_text text="data_tables"/>
65 <has_text text="bakta_database"/>
66 <has_text text="bakta_version"/>
67 <has_text text="V5.0light_2023-06-08"/>
68 </assert_contents>
69 </output>
70 </test>
71 <!-- Test 3 with light db -->
72 <test expect_num_outputs="1">
73 <param name="test_data_manager" value=""/>
74 <param name="database_select" value="5.1_light"/>
75 <output name="output_file" ftype="data_manager_json">
76 <assert_contents>
77 <has_text text="data_tables"/>
78 <has_text text="bakta_database"/>
79 <has_text text="bakta_version"/>
80 <has_text text="V5.1light_2024-01-19"/>
81 </assert_contents>
82 </output>
49 </test> 83 </test>
50 </tests> 84 </tests>
51 <help><![CDATA[ 85 <help><![CDATA[
52 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database> 86 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>
53 ]]></help> 87 ]]></help>