Mercurial > repos > dave > data_manager_build_kraken2_database
diff data_manager/kraken2_build_database.xml @ 0:bd47b9f87d67 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
| author | dave |
|---|---|
| date | Tue, 01 Dec 2020 16:07:40 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_database.xml Tue Dec 01 16:07:40 2020 +0000 @@ -0,0 +1,116 @@ +<?xml version="1.0"?> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="18.09"> + <macros> + <token name="@TOOL_VERSION@">2.1.1</token> + <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" /> + <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" /> + <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> + </xml> + </macros> + <description>database builder</description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> + <requirement type="package" version="3.7">python</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-release $database_type.kraken_release + #if $database_type.kraken_release == "April_2019": + --minikraken2-version ${database_type.kraken_release.minikraken2_version} + #end if + #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} + --load-factor ${database_type.load_factor} + ${database_type.clean} + #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} + --load-factor ${database_type.load_factor} + ${database_type.clean} + #else if $database_type.database_type == "custom" + --threads \${GALAXY_SLOTS:-1} + ${database_type.skip_maps} + --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} + --load-factor ${database_type.load_factor} + ${database_type.clean} + #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"> + <conditional name="kraken_release"> + <param name="minikraken2_release" type="select" multiple="false" label="Select the MiniKraken2 release to download"> + <option value="April_2019">April 2019</option> + <option value="March_2020">March 2020</option> + </param> + <when value="April_2019"> + <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="March_2020" /> + </conditional> + </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" /> + <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> + <expand macro="common_params" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="database_type" value="custom" /> + <param name="custom_fasta" value="adapter.fa" /> + <param name="custom_database_name" value="database" /> + <param name="skip_maps" value="true" /> + <output name="out_file" value="kraken2_custom_data_manager.json" /> + </test> + </tests> + <help> + </help> + <citations> + <citation type="doi">10.1186/gb-2014-15-3-r46</citation> + </citations> +</tool>