Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

comparison data_manager/plasmidfinder_fetch_database.xml @ 0:8ad77a9dc91d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
author pimarin
date Tue, 14 Feb 2023 14:25:43 +0000
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children 9ef108e34063
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-1:000000000000 0:8ad77a9dc91d
1 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>plasmidfinder database builder</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/plasmidfinder_fetch_database.py'
10 --db_version '$database_select'
11 '$output_file'
12 ]]></command>
13 <inputs>
14 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
15 <option value="latest" selected="true">Latest available version</option>
16 <option value="2.1">V2.1_2019-08-28</option>
17 </param>param>
18 </inputs>
19 <outputs>
20 <data name="output_file" format="data_manager_json"/>
21 </outputs>
22 <tests>
23 <!-- Test_1 DB latest -->
24 <test expect_num_outputs="1">
25 <param name="database_select" value="latest"/>
26 <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
27 <assert_contents>
28 <has_text_matching expression='{"data_tables": {"plasmidfinder_database": [{"date": "\d\d\d\d-\d\d-\d\d", "name": "b1c9ddac0e61_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_b1c9ddac0e61_\d\d\d\d-\d\d-\d\d"' />
29 </assert_contents>
30 </output>
31 </test>
32 <!-- Test_2 DB 2.1 -->
33 <test expect_num_outputs="1">
34 <param name="database_select" value="2.1"/>
35 <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
36 <assert_contents>
37 <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-db", "value": "plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d"' />
38 </assert_contents>
39 </output>
40 </test>
41 </tests>
42 <help><![CDATA[
43 Download plasmidfinder database from the bitbucket repository
44 ]]></help>
45 <citations>
46 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
47 </citations>
48 </tool>