| Previous changeset 0:c2e4127fb5bf (2019-10-20) Next changeset 2:fd5830f88314 (2020-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a" |
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modified:
data_manager/bracken_build_database.xml tool_data_table_conf.xml.test |
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added:
test-data/bracken_databases.loc |
| b |
| diff -r c2e4127fb5bf -r 9059edc96a85 data_manager/bracken_build_database.xml --- 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 |
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| @@ -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 ${read_len} |
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| diff -r c2e4127fb5bf -r 9059edc96a85 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Sun Oct 20 09:37:21 2019 -0400 +++ b/tool_data_table_conf.xml.test Sun Jan 19 04:33:53 2020 -0500 |
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| @@ -5,4 +5,9 @@ <columns>value, name, path</columns> <file path="${__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> |