Mercurial > repos > pimarin > data_manager_bakta
comparison data_manager/bakta_build_database.xml @ 1:faae5d8ce0cb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
author | pimarin |
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date | Thu, 27 Oct 2022 13:54:13 +0000 |
parents | 9d08486abf8e |
children | decc1723cf97 |
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0:9d08486abf8e | 1:faae5d8ce0cb |
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1 <?xml version="1.0"?> | 1 |
2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
3 <description> Bakta database builder </description> | 3 <description> Bakta database builder </description> |
4 <macros> | 4 <macros> |
5 <import>macro.xml</import> | 5 <import>macro.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 | |
9 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
10 python '$__tool_directory__/bakta_build_database.py' | 11 python '$__tool_directory__/bakta_build_database.py' |
11 #if $database_command == "download" | 12 '$output_file' |
12 download --output $output_file | 13 --database_version '$database_select' |
13 #else if $database_command == "update" | |
14 #else if $database_command == "update" | |
15 update --db $output_file | |
16 #end if | |
17 ]]></command> | 14 ]]></command> |
18 <inputs> | 15 <inputs> |
19 <conditional> | 16 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)" > |
20 <param name="database_command" type="select" label="Database action" multiple="false" help="Action on bakta database. Install or update database"> | 17 <option value="1.0"> V1.0_2020-11-20 </option> |
21 <option value="download"> Download a prebuild bakta database</option> | 18 <option value="1.1"> V1.1_2020-12-18 </option> |
22 <option value="custom"> Download a custom database</option> | 19 <option value="2.0"> V2.0_2021-04-05 </option> |
23 <option value="update"> Update the databases</option> | 20 <option value="3.0"> V3.0_2021-08-05 </option> |
24 </param> | 21 <option value="3.1"> V3.1_2022-02-03 </option> |
25 <when value="download"/> | 22 <option value="4.0" selected="true" > V4.0_2022-08-29 </option> |
26 <when value="update"/> | 23 <option value="test"> database_test </option> |
27 <when value="custom"> | 24 </param> |
28 <param name="db_link"></param> | |
29 </when> | |
30 </conditional> | |
31 </inputs> | 25 </inputs> |
32 <outputs> | 26 <outputs> |
33 <data name="output_file" format="data_manager_json" /> | 27 <data name="output_file" format="data_manager_json" /> |
34 </outputs> | 28 </outputs> |
35 <tests> | 29 <tests> |
36 | 30 <!-- Test download --> |
37 <!-- TEST2 update --> | |
38 <test expect_num_outputs="1"> | 31 <test expect_num_outputs="1"> |
39 <param name="database_command" value="update"/> | 32 <param name="database_select" value="test"/> |
40 <output name="output_file"> | 33 <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/> |
41 <assert_contents> | |
42 <has_text text="pangoLEARN data release 2021-04-01"/> | |
43 <has_text text='"format_version": "1.0"'/> | |
44 </assert_contents> | |
45 </output> | |
46 </test> | 34 </test> |
47 </tests> | 35 </tests> |
48 <help><![CDATA[ | 36 <help><![CDATA[ |
49 Download, update or list bakta databases <https://github.com/oschwengers/bakta#database> | 37 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database> |
50 ]]></help> | 38 ]]></help> |
51 <citations> | 39 <citations> |
52 <citation type="doi">10.1099/mgen.0.000685</citation> | 40 <citation type="doi">10.1099/mgen.0.000685</citation> |
53 </citations> | 41 </citations> |
54 </tool> | 42 </tool> |