Mercurial > repos > dfornika > data_manager_build_kraken2_database
view data_manager/kraken2_build_database.xml @ 17:4c9f9d6098eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
author | dfornika |
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date | Mon, 06 May 2019 19:42:14 -0400 |
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children | f005b6efd096 |
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<?xml version="1.0"?> <tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta"> <macros> <xml name="common_params"> <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" /> </xml> </macros> <description>database builder</description> <requirements> <requirement type="package" version="2.0.8_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_database.py' '${out_file}' --database-type ${database_type.database_type} #if $database_type.database_type == "minikraken" --minikraken2-version ${database_type.minikraken2_version} #else if $database_type.database_type == "standard" --threads \${GALAXY_SLOTS:-1} --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} #else if $database_type.database_type == "special" --threads \${GALAXY_SLOTS:-1} --special-database-type ${database_type.special_database_type} --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} #else if $database_type.database_type == "custom" --threads \${GALAXY_SLOTS:-1} --custom-fasta ${database_type.custom_fasta} --custom-database-name ${database_type.custom_database_name} --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} #end if ]]> </command> <inputs> <conditional name="database_type"> <param name="database_type" type="select" multiple="false" label="Database Type"> <option value="standard">Standard</option> <option value="minikraken">MiniKraken</option> <option value="special">Special</option> <option value="custom">Custom</option> </param> <when value="standard"> <expand macro="common_params" /> </when> <when value="minikraken"> <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> <option value="v2">Version 2</option> <option value="v1">Version 1</option> </param> </when> <when value="special"> <param name="special_database_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> <expand macro="common_params" /> </when> <when value="custom"> <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> <param name="custom_database_name" type="text" label="Name for this database" /> <expand macro="common_params" /> </when> </conditional> </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>