Mercurial > repos > pimarin > data_manager_bakta

comparison data_manager/bakta_build_database.xml @ 11:c50e8b4f74d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
author pimarin
date Wed, 02 Nov 2022 11:06:36 +0000
parents 683b09c92299
children 7bd60bfa8ffc
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10:9c65e5da43e2 11:c50e8b4f74d7
1 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
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 mkdir './output_dir_json' &&
12 ln -s '$output_file' './output_dir_json/json_output.json' &&
13 python '$__tool_directory__/bakta_build_database.py' 11 python '$__tool_directory__/bakta_build_database.py'
14 './output_dir_json/json_output.json' 12 '$output_file'
15 --database_version '$database_select' 13 --database_version '$database_select'
14 '$test_data_manager'
16 ]]></command> 15 ]]></command>
17 <inputs> 16 <inputs>
18 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)" > 17 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
19 <option value="latest" selected="true" > Latest available version </option> 18 <option value="latest" selected="true">Latest available version</option>
20 <option value="1.0"> V1.0_2020-11-20 </option> 19 <option value="1.0">V1.0_2020-11-20</option>
21 <option value="1.1"> V1.1_2020-12-18 </option> 20 <option value="1.1">V1.1_2020-12-18</option>
22 <option value="2.0"> V2.0_2021-04-05 </option> 21 <option value="2.0">V2.0_2021-04-05</option>
23 <option value="3.0"> V3.0_2021-08-05 </option> 22 <option value="3.0">V3.0_2021-08-05</option>
24 <option value="3.1"> V3.1_2022-02-03 </option> 23 <option value="3.1">V3.1_2022-02-03</option>
25 <option value="4.0"> V4.0_2022-08-29 </option> 24 <option value="4.0">V4.0_2022-08-29</option>
26 <option value="test"> database_test </option>
27 </param> 25 </param>
26 <param name="test_data_manager" type="hidden" value=""/>
28 </inputs> 27 </inputs>
29 <outputs> 28 <outputs>
30 <data name="output_file" format="data_manager_json" from_work_dir="./output_dir_json/json_output.json"/> 29 <data name="output_file" format="data_manager_json"/>
31 </outputs> 30 </outputs>
32 <tests> 31 <tests>
33 <!-- Test download --> 32 <!-- Test download -->
34 <test expect_num_outputs="1"> 33 <test expect_num_outputs="1">
35 <param name="database_select" value="test"/> 34 <param name="test_data_manager" value="--test"/>
36 <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/> 35 <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/>
37 </test> 36 </test>
38 </tests> 37 </tests>
39 <help><![CDATA[ 38 <help><![CDATA[
40 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database> 39 Download specific version of Bakta database <https://github.com/oschwengers/bakta#database>