Mercurial > repos > iuc > data_manager_fetch_plasmidfinder
diff data_manager/plasmidfinder_fetch_database.xml @ 0:b56071bdecad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
| author | iuc |
|---|---|
| date | Thu, 15 Jun 2023 09:14:08 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/plasmidfinder_fetch_database.xml Thu Jun 15 09:14:08 2023 +0000 @@ -0,0 +1,39 @@ +<tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>plasmidfinder database builder</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/plasmidfinder_fetch_database.py' + --db_version '$database_select' + '$output_file' + ]]></command> + <inputs> + <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)"> + <option value="latest" selected="true">Latest available version</option> + <option value="2.1">V2.1_2019-08-28</option> + </param> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json"/> + </outputs> + <tests> + <!-- Test_2 DB 2.1 --> + <test expect_num_outputs="1"> + <param name="database_select" value="2.1"/> + <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json"> + <assert_contents> + <has_text text="2019_08_28"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Download plasmidfinder database from the bitbucket repository: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/ + ]]></help> + <citations> + <citation type="doi">10.1007/978-1-4939-9877-7_20</citation> + </citations> +</tool>
