Mercurial > repos > dfornika > data_manager_build_bracken_database
view data_manager/bracken_build_database.xml @ 11:2a4d2363ebb9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3-dirty"
author | dfornika |
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date | Thu, 04 Nov 2021 21:48:22 +0000 |
parents | 92f9975f08e2 |
children | bd5a161cce7c |
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<?xml version="1.0"?> <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy1" profile="19.01"> <description>bracken database builder</description> <requirements> <requirement type="package" version="2.5">bracken</requirement> <requirement type="package" version="2.1.1">kraken2</requirement> </requirements> <command> <![CDATA[ #import os #set db_dir = os.path.basename($kraken_db.fields.path) mkdir '$db_dir' && ln -s '${kraken_db.fields.path}'/* '$db_dir/' && python '$__tool_directory__/bracken_build_database.py' '${out_file}' --kraken-db '$db_dir' --threads \${GALAXY_SLOTS:-1} --kmer-len ${kmer_len} --read-len ${read_len} --database-name '${database_name}' ]]> </command> <inputs> <param name="kraken_db" type="select"> <options from_data_table="kraken2_databases"> <validator type="no_options" message="No Kraken2 databases are available" /> </options> </param> <conditional name="check_prebuilt"> <param name="prebuilt" type="boolean" checked="false" truevalue="--prebuilt" falsevalue="" label="Use Pre-built DB" /> <when value="false"> <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> </when> </conditional> <param name="database_name" type="text" label="Database Name" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> <param name="kraken_db" value="test_entry" /> <param name="database_name" value="database" /> <output name="out_file"> <assert_contents> <has_text text="test_db/database100mers.kmer_distrib" /> </assert_contents> </output> </test> </tests> <help> </help> <citations> <citation type="doi">10.7717/peerj-cs.104</citation> </citations> </tool>