Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder
comparison data_manager/plasmidfinder_fetch_database.xml @ 5:60cfd33bc2fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 0a3992c5be846fc9f18b7ca18f0adcd78f5b9396-dirty
author | pimarin |
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date | Mon, 24 Jul 2023 10:00:33 +0000 (21 months ago) |
parents | 5ffc68b4ec04 |
children | 4e933a39094f |
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4:e05fd47bcca6 | 5:60cfd33bc2fb |
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2 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
3 <description>plasmidfinder database builder</description> | 2 <description>plasmidfinder database builder</description> |
4 <macros> | 3 <macros> |
5 <import>macro.xml</import> | 4 <import>macro.xml</import> |
6 </macros> | 5 </macros> |
8 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
9 <![CDATA[ | 8 <![CDATA[ |
10 python '$__tool_directory__/plasmidfinder_fetch_database.py' | 9 python '$__tool_directory__/plasmidfinder_fetch_database.py' |
11 --db_version '$database_select' | 10 --db_version '$database_select' |
12 '$output_file' | 11 '$output_file' |
12 && cat '$output_file' | |
13 ]]></command> | 13 ]]></command> |
14 <inputs> | 14 <inputs> |
15 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> | 15 <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> | 16 <option value="latest" selected="true">Latest available version</option> |
17 <option value="2.1">V2.1_2019-08-28</option> | 17 <option value="2.1">V2.1_2019-08-28</option> |
18 </param>param> | 18 </param> |
19 </inputs> | 19 </inputs> |
20 <outputs> | 20 <outputs> |
21 <data name="output_file" format="data_manager_json"/> | 21 <data name="output_file" format="data_manager_json"/> |
22 </outputs> | 22 </outputs> |
23 <tests> | 23 <tests> |
24 <!-- Test_1 DB latest --> | 24 <!-- Test_2 DB 2.1 --> |
25 <test expect_num_outputs="1"> | 25 <test expect_num_outputs="1"> |
26 <param name="database_select" value="latest"/> | 26 <param name="database_select" value="2.1"/> |
27 <output name="output_file" value="plasmidfinder_test_data_manager_latest.json"> | 27 <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json"> |
28 <assert_contents> | 28 <assert_contents> |
29 <has_text_matching expression="\{"data_tables"\:\ {"plasmidfinder_database"\:\ \[\{"date"\:\ "\d\d\d\d-\d\d-\d\d",\ "name"\:\ "\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d",\ "path"\:\ "plasmidfinder_database",\ "value"\:\ "plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d"\}\]\}\}"/> | 29 <has_text text="2019_08_28"/> |
30 </assert_contents> | 30 </assert_contents> |
31 </output> | 31 </output> |
32 </test> | |
33 <!-- Test_2 DB 2.1 --> | |
34 <test expect_num_outputs="1"> | |
35 <param name="database_select" value="2.1"/> | |
36 <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json"> | |
37 <assert_contents> | |
38 <has_text_matching expression="\{"data_tables"\:\ {"plasmidfinder_database":\ \[\{"date"\:\ "\d\d\d\d-\d\d-\d\d",\ "name"\:\ "2.1_\d\d\d\d-\d\d-\d\d",\ "path"\:\ "plasmidfinder_database",\ "value"\:\ "plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d"\}\]\}\}"/> | |
39 </assert_contents> | |
40 </output> | |
41 </test> | 32 </test> |
42 </tests> | 33 </tests> |
43 <help><![CDATA[ | 34 <help><![CDATA[ |
44 Download plasmidfinder database from the bitbucket repository | 35 Download plasmidfinder database from the bitbucket repository: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/ |
45 ]]></help> | 36 ]]></help> |
46 <citations> | 37 <citations> |
47 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> | 38 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> |
48 </citations> | 39 </citations> |
49 </tool> | 40 </tool> |