Mercurial > repos > dfornika > data_manager_build_bracken_database
view data_manager/bracken_build_database.xml @ 8:891f564fd6e3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
author | dfornika |
---|---|
date | Tue, 15 Oct 2019 16:59:44 -0400 |
parents | cc49eb0defee |
children | 472b3834d65d |
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<?xml version="1.0"?> <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5"> <description>bracken database builder</description> <requirements> <requirement type="package" version="2.5">bracken</requirement> <requirement type="package" version="2.0.8_beta">kraken2</requirement> </requirements> <version_command>bracken --version</version_command> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/bracken_build_database.py' '${out_file}' --kraken-db ${kraken_db.fields.path} --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> <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" /> <param name="database_name" type="text" label="Database Name" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <help> </help> <citations> <citation type="doi">10.7717/peerj-cs.104</citation> </citations> </tool>