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
date Mon, 24 Jul 2023 10:00:33 +0000 (21 months ago)
parents 5ffc68b4ec04
children 4e933a39094f
comparison
equal deleted inserted replaced
4:e05fd47bcca6 5:60cfd33bc2fb
1
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="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;\:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/> 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="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;2.1_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/>
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>