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view data_manager/kraken2_standard_database_builder.xml @ 3:b03007bc0f05 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 18:55:04 -0500 |
parents | 7e43f66abe9d |
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<?xml version="1.0"?> <tool id="kraken2_standard_database_builder" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.7_beta"> <description>database builder</description> <requirements> <requirement type="package" version="2.0.7_beta">kraken2</requirement> </requirements> <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> <command detect_errors="exit_code"> <![CDATA[ #import datetime #set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d') + "_standard" mkdir kraken2-database && cd kraken2-database && kraken2-build --standard --threads \${GALAXY_SLOTS:-1} --db '${kraken2_db_name}' --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} --minimizer-spaces ${minimizer_spaces} && cd .. && python '$__tool_directory__/make_json.py' --db '${kraken2_db_name}' --out '${out_file}' ]]> </command> <inputs> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <help> </help> <citations> <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </tool>