Mercurial > repos > iuc > data_manager_cat
view data_manager/data_manager_cat.xml @ 2:472dabcb03bf draft default tip
planemo upload commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author | iuc |
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date | Mon, 18 Dec 2023 09:36:10 +0000 |
parents | cffd8e2382cf |
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<tool id="data_manager_cat" name="CAT DB" version="5.0.3.1" tool_type="manage_data" profile="18.09"> <description>Install a new CAT database</description> <requirements> <requirement type="package" version="5.0.3">cat</requirement> </requirements> <version_command><![CDATA[ CAT --version ]]></version_command> <command detect_errors="exit_code"><![CDATA[ mkdir -p '$out_file.extra_files_path' && python '${__tool_directory__}/data_manager_cat.py' --config_file '$out_file' --install_path '$out_file.extra_files_path' #if $db.src == 'download' --db_url '$db.db_url' #end if ]]></command> <inputs> <conditional name="db"> <param name="src" type="select" label="Download or Build DBs"> <option value="download">download</option> <option value="build">build</option> </param> <when value="download"> <param name="db_url" type="text" label="DB URL at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/" help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz"> </param> </when> <when value="build"> </when> </conditional> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> <test> <conditional name="db"> <param name="src" value="download"/> <param name="db_url" value="https://github.com/galaxyproject/tools-iuc/blob/ce82f787f1f035debfc86de09a271a9ec8d27e0e/data_managers/data_manager_cat/test-data/CAT_prepare_test.tar.gz?raw=true"/> </conditional> <output name="out_file"> <assert_contents> <has_text text="CAT_prepare_test/taxonomy" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ This tool prepares reference data for CAT, the Contig Annotation Tool. It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/ or build new reference data using the CAT prepare application. This requires at least 100GB of RAM, 250GB of disk space, and 24 hours. ]]></help> <citations> <citation type="doi">https://doi.org/10.1101/072868</citation> <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation> <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation> </citations> </tool>