Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 6:2ea60e272b90 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9b4d704c147761201fa9f1450fcf5ba6871104d8-dirty
| author | dfornika |
|---|---|
| date | Wed, 27 Feb 2019 21:50:03 -0500 |
| parents | 2eb7850c7434 |
| children | 1088e1592527 |
| files | data_manager/kraken2_standard_database_builder.xml |
| diffstat | 1 files changed, 8 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 21:32:42 2019 -0500 +++ b/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 21:50:03 2019 -0500 @@ -7,16 +7,18 @@ <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> <command detect_errors="exit_code"> <![CDATA[ - #set kraken2_db_name = datetime.datetime.today().strftime('%Y-%m-%d') + #import datetime + #set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d') mkdir kraken2_database && cd kraken2_database && kraken2-build \ --standard \ - --db ${kraken2_db_name} \ - --kmer-len ${kmer_len} \ - --minimizer-len ${minimizer_len} \ - --minimizer-spaces ${minimizer_spaces} && + --threads \${GALAXY_SLOTS:-1} \ + --db '${kraken2_db_name}' \ + --kmer-len '${kmer_len}' \ + --minimizer-len '${minimizer_len}' \ + --minimizer-spaces '${minimizer_spaces}' && cd .. && - python '$__tool_directory__/make_json.py' --db ${kraken2_db_name} --out '${out_file}' + python '$__tool_directory__/make_json.py' --db '${kraken2_db_name}' --out '${out_file}' ]]> </command> <inputs>