Mercurial > repos > pimarin > data_manager_bakta
diff 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 |
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--- a/data_manager/bakta_build_database.xml Wed Aug 17 14:42:22 2022 +0000 +++ b/data_manager/bakta_build_database.xml Thu Oct 27 13:54:13 2022 +0000 @@ -1,4 +1,4 @@ -<?xml version="1.0"?> + <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> Bakta database builder </description> <macros> @@ -6,47 +6,35 @@ </macros> <expand macro="requirements"/> <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ python '$__tool_directory__/bakta_build_database.py' - #if $database_command == "download" - download --output $output_file - #else if $database_command == "update" - #else if $database_command == "update" - update --db $output_file - #end if + '$output_file' + --database_version '$database_select' ]]></command> <inputs> - <conditional> - <param name="database_command" type="select" label="Database action" multiple="false" help="Action on bakta database. Install or update database"> - <option value="download"> Download a prebuild bakta database</option> - <option value="custom"> Download a custom database</option> - <option value="update"> Update the databases</option> - </param> - <when value="download"/> - <when value="update"/> - <when value="custom"> - <param name="db_link"></param> - </when> - </conditional> + <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)" > + <option value="1.0"> V1.0_2020-11-20 </option> + <option value="1.1"> V1.1_2020-12-18 </option> + <option value="2.0"> V2.0_2021-04-05 </option> + <option value="3.0"> V3.0_2021-08-05 </option> + <option value="3.1"> V3.1_2022-02-03 </option> + <option value="4.0" selected="true" > V4.0_2022-08-29 </option> + <option value="test"> database_test </option> + </param> </inputs> <outputs> <data name="output_file" format="data_manager_json" /> </outputs> <tests> - - <!-- TEST2 update --> + <!-- Test download --> <test expect_num_outputs="1"> - <param name="database_command" value="update"/> - <output name="output_file"> - <assert_contents> - <has_text text="pangoLEARN data release 2021-04-01"/> - <has_text text='"format_version": "1.0"'/> - </assert_contents> - </output> + <param name="database_select" value="test"/> + <output name="output_file" value="bakta_test_data_manager.json" compare="contains"/> </test> </tests> <help><![CDATA[ - Download, update or list bakta databases <https://github.com/oschwengers/bakta#database> + Download specific version of Bakta database <https://github.com/oschwengers/bakta#database> ]]></help> <citations> <citation type="doi">10.1099/mgen.0.000685</citation>