Mercurial > repos > iuc > data_manager_fetch_busco_options
comparison data_manager/busco_options.xml @ 0:4e3bbaa0b70f 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 13:12:07 +0000 |
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| -1:000000000000 | 0:4e3bbaa0b70f |
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| 1 <tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <token name="@TOOL_VERSION@">5.8.0</token> | |
| 5 <token name="@VERSION_SUFFIX@">0</token> | |
| 6 </macros> | |
| 7 <requirements> | |
| 8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 #if $test: | |
| 12 busco --download_path test/ --download virus > /dev/null && | |
| 13 #set db_path="./test" | |
| 14 #else | |
| 15 #set db_path=$cached_db.fields.path | |
| 16 #end if | |
| 17 python '$__tool_directory__/extract.py' '$db_path' '$cached_db' '$out_file' | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 20 <param name="test" type="hidden"/> | |
| 21 <param name="cached_db" label="Cached database with lineage" type="select"> | |
| 22 <options from_data_table="busco_database"> | |
| 23 <validator message="No BUSCO database is available" type="no_options"/> | |
| 24 </options> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="out_file" format="data_manager_json" label="BUSCO options data manager: JSON"/> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test expect_num_outputs="1"> | |
| 32 <param name="test" value="true"/> | |
| 33 <param name="cached_db" value="test"/> | |
| 34 <output name="out_file"> | |
| 35 <assert_contents> | |
| 36 <has_text text="busco_database_options"/> | |
| 37 <has_text text="Chordopoxvirinae"/> | |
| 38 <has_text text="chordopoxvirinae_"/> | |
| 39 </assert_contents> | |
| 40 </output> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help>This tool determines the possible choices of BUSCO lineages in a given BUSCO DB.</help> | |
| 44 <citations> | |
| 45 <citation type="doi">10.1093/bioinformatics/btv351</citation> | |
| 46 </citations> | |
| 47 </tool> |