Mercurial > repos > dfornika > data_manager_build_kraken2_database
view data_manager/kraken2_build_custom.xml @ 5:1f6fe9dc5490 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
author | dfornika |
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date | Mon, 04 Mar 2019 18:59:44 -0500 |
parents | 988c436ad798 |
children | ce101123d015 |
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<?xml version="1.0"?> <tool id="kraken2_build_custom" name="Kraken2 Custom Database Builder (subprocess)" 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 $NF}'</version_command> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/kraken2_build_custom.py' '${out_file}' --threads \${GALAXY_SLOTS:-1} --db ${database_name} --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} --minimizer-spaces ${minimizer_spaces} --fasta ${input_fasta} ]]> </command> <inputs> <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> <param name="database_name" type="text" label="Name for this database" /> <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>