Mercurial > repos > iuc > data_manager_build_bracken_database
changeset 1:9059edc96a85 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
| author | iuc |
|---|---|
| date | Sun, 19 Jan 2020 04:33:53 -0500 |
| parents | c2e4127fb5bf |
| children | fd5830f88314 |
| files | data_manager/bracken_build_database.xml test-data/bracken_databases.loc tool_data_table_conf.xml.test |
| diffstat | 2 files changed, 11 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/bracken_build_database.xml Sun Oct 20 09:37:21 2019 -0400 +++ b/data_manager/bracken_build_database.xml Sun Jan 19 04:33:53 2020 -0500 @@ -7,9 +7,14 @@ </requirements> <command> <![CDATA[ + #import os + #set db_dir = os.path.basename($kraken_db.fields.path) + + mkdir '$db_dir' && + ln -s '${kraken_db.fields.path}'/* '$db_dir/' && python '$__tool_directory__/bracken_build_database.py' '${out_file}' - --kraken-db '${kraken_db.fields.path}' + --kraken-db '$db_dir' --threads \${GALAXY_SLOTS:-1} --kmer-len ${kmer_len} --read-len ${read_len}
--- a/tool_data_table_conf.xml.test Sun Oct 20 09:37:21 2019 -0400 +++ b/tool_data_table_conf.xml.test Sun Jan 19 04:33:53 2020 -0500 @@ -5,4 +5,9 @@ <columns>value, name, path</columns> <file path="${__HERE__}/test-data/kraken2_databases.loc" /> </table> + <!-- Locations of bracken databases in the required format --> + <table name="bracken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/bracken_databases.loc" /> + </table> </tables>