Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_custom_database_builder.xml @ 0:7e43f66abe9d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
| author | dfornika |
|---|---|
| date | Thu, 28 Feb 2019 02:32:38 -0500 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_custom_database_builder.xml Thu Feb 28 02:32:38 2019 -0500 @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool id="kraken2_custom_database_builder" name="Kraken2 Custom 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[ + #set $library_list = str($libraries).split(',') + mkdir kraken2-database && cd kraken2-database && + kraken2-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' && + #for $library in $library_list: + #if str($library) != 'None': + kraken2-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' && + #end if + #end for + #for $fasta in $input_fasta: + #if str($fasta) != 'None': + kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' && + #end if + #end for + kraken2-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && + cd .. && + python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}' + ]]> + </command> + <inputs> + <param name="database_name" type="text" label="Name for this database" /> + <param name="libraries" type="select" multiple="true" label="Select partial library to download"> + <option value="archaea">Archaea</option> + <option value="bacteria">Bacteria</option> + <option value="plasmid">Plasmid</option> + <option value="viral">Viral</option> + <option value="human">Human</option> + </param> + <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> + <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>