Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_special.xml @ 7:ae6180bdb1e9 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author | dfornika |
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date | Mon, 04 Mar 2019 19:20:33 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_special.xml Mon Mar 04 19:20:33 2019 -0500 @@ -0,0 +1,37 @@ +<?xml version="1.0"?> +<tool id="kraken2_build_special" name="Kraken2 Special 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 $NF}'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/kraken2_build_special.py' + '${out_file}' + --db-type ${db_type} + --threads \${GALAXY_SLOTS:-1} + --kmer-len ${kmer_len} + --minimizer-len ${minimizer_len} + --minimizer-spaces ${minimizer_spaces} + ]]> + </command> + <inputs> + <param name="db_type" type="select" multiple="false" label="Select database to build"> + <option value="greengenes">Greengenes</option> + <option value="silva">Silva</option> + <option value="rdp">RDP</option> + </param> + <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>