Mercurial > repos > pimarin > data_manager_bakta
comparison data_manager/bakta_build_database.xml @ 0:9d08486abf8e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
| author | pimarin |
|---|---|
| date | Wed, 17 Aug 2022 14:42:22 +0000 |
| parents | |
| children | faae5d8ce0cb |
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| -1:000000000000 | 0:9d08486abf8e |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="bakta_build_database" name="Bakta" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 3 <description> Bakta database builder </description> | |
| 4 <macros> | |
| 5 <import>macro.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="version_command"/> | |
| 9 <command detect_errors="aggressive"><![CDATA[ | |
| 10 python '$__tool_directory__/bakta_build_database.py' | |
| 11 #if $database_command == "download" | |
| 12 download --output $output_file | |
| 13 #else if $database_command == "update" | |
| 14 #else if $database_command == "update" | |
| 15 update --db $output_file | |
| 16 #end if | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <conditional> | |
| 20 <param name="database_command" type="select" label="Database action" multiple="false" help="Action on bakta database. Install or update database"> | |
| 21 <option value="download"> Download a prebuild bakta database</option> | |
| 22 <option value="custom"> Download a custom database</option> | |
| 23 <option value="update"> Update the databases</option> | |
| 24 </param> | |
| 25 <when value="download"/> | |
| 26 <when value="update"/> | |
| 27 <when value="custom"> | |
| 28 <param name="db_link"></param> | |
| 29 </when> | |
| 30 </conditional> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="output_file" format="data_manager_json" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 | |
| 37 <!-- TEST2 update --> | |
| 38 <test expect_num_outputs="1"> | |
| 39 <param name="database_command" value="update"/> | |
| 40 <output name="output_file"> | |
| 41 <assert_contents> | |
| 42 <has_text text="pangoLEARN data release 2021-04-01"/> | |
| 43 <has_text text='"format_version": "1.0"'/> | |
| 44 </assert_contents> | |
| 45 </output> | |
| 46 </test> | |
| 47 </tests> | |
| 48 <help><![CDATA[ | |
| 49 Download, update or list bakta databases <https://github.com/oschwengers/bakta#database> | |
| 50 ]]></help> | |
| 51 <citations> | |
| 52 <citation type="doi">10.1099/mgen.0.000685</citation> | |
| 53 </citations> | |
| 54 </tool> |