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view data_manager/pharokka_db_fetcher.xml @ 1:50caca83e7c9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit fcbcfe6bfcf007dc489ae035a6f23c07dc64ed31
author | iuc |
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date | Sun, 06 Aug 2023 10:11:42 +0000 |
parents | 97f310b8e308 |
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<?xml version="1.0"?> <tool id="pharokka_db_fetcher" name="phrokka DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Fetches the DB required for phrokka</description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools" /> <expand macro="requirements" /> <expand macro="version" /> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/data_manager_fetch_pharokka_db.py' --out '${out_file}' --version '${version}' $test_data_manager ]]> </command> <inputs> <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." /> <!-- <param name="test_data_manager" type="text" value=""/> --> <param argument="--version" type="text" value="1.2.0" help="Check https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 for current version. The default value is recommended."/> </inputs> <outputs> <data format="data_manager_json" name="out_file" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="test_data_manager" value="--test"/> <param name="version" value="v1.2.0"/> <output name="out_file"> <assert_contents> <has_text text="Pharokka DB version"/> <has_text text="db_from_"/> <has_text text="pharokka_db"/> <has_text text="v1.2.0"/> </assert_contents> </output> </test> </tests> <help> <![CDATA[ Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. This data manager fetches the DB using the build-in tool download script. The version must be checked here: https://github.com/gbouras13/pharokka/blob/c822b4c3b8cf642512a5c236fc4036ad53f48587/bin/databases.py#L102 ]]> </help> <expand macro="citations" /> <expand macro="creator" /> </tool>