Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_custom.xml @ 2:cf0cda80b659 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author | dfornika |
---|---|
date | Thu, 28 Feb 2019 18:18:01 -0500 |
parents | |
children | 988c436ad798 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_custom.xml Thu Feb 28 18:18:01 2019 -0500 @@ -0,0 +1,33 @@ +<?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_standard.py' + '${out_file}' + --threads \${GALAXY_SLOTS:-1} + --fasta ${input_fasta} + --kmer-len ${kmer_len} + --minimizer-len ${minimizer_len} + --minimizer-spaces ${minimizer_spaces} + ]]> + </command> + <inputs> + <param name="input_fasta" type="data" format="fasta" multiple="False" 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>