Mercurial > repos > iuc > data_manager_fetch_busco
diff data_manager/busco_options.xml @ 8:29548c43fb33 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
| author | iuc |
|---|---|
| date | Tue, 22 Apr 2025 13:11:38 +0000 |
| parents | 83c7f3907ad2 |
| children |
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--- a/data_manager/busco_options.xml Fri Apr 04 11:17:37 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> - <description></description> - <macros> - <token name="@TOOL_VERSION@">5.8.0</token> - <token name="@VERSION_SUFFIX@">0</token> - </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">busco</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - #if $test: - busco --download_path test/ --download virus > /dev/null && - #set db_path="./test" - #else - #set db_path=$cached_db.fields.path - #end if - python '$__tool_directory__/extract.py' '$db_path' '$cached_db' '$out_file' - ]]></command> - <inputs> - <param name="test" type="hidden"/> - <param name="cached_db" label="Cached database with lineage" type="select"> - <options from_data_table="busco_database"> - <validator message="No BUSCO database is available" type="no_options"/> - </options> - </param> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" label="BUSCO options data manager: JSON"/> - </outputs> - <tests> - <test expect_num_outputs="1"> - <param name="test" value="true"/> - <param name="cached_db" value="test"/> - <output name="out_file"> - <assert_contents> - <has_text text="busco_database_options"/> - <has_text text="Chordopoxvirinae"/> - <has_text text="chordopoxvirinae_"/> - </assert_contents> - </output> - </test> - </tests> - <help>This tool determines the possible choices of BUSCO lineages in a given BUSCO DB.</help> - <citations> - <citation type="doi">10.1093/bioinformatics/btv351</citation> - </citations> -</tool>