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
date Thu, 27 Oct 2022 13:54:13 +0000
parents 9d08486abf8e
children decc1723cf97
comparison
equal deleted inserted replaced
0:9d08486abf8e 1:faae5d8ce0cb
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>