Mercurial > repos > dfornika > data_manager_build_bracken_database
changeset 6:f25264bb7d6d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit 324b55b24e9d403b04a1cc6aba362b03bad98368-dirty
| author | dfornika |
|---|---|
| date | Wed, 31 Jul 2019 18:08:06 -0400 |
| parents | 0a2f97661db3 |
| children | cc49eb0defee |
| files | data_manager/bracken_build_database.py data_manager_conf.xml |
| diffstat | 2 files changed, 5 insertions(+), 11 deletions(-) [+] |
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--- a/data_manager/bracken_build_database.py Fri Jul 26 17:18:22 2019 -0400 +++ b/data_manager/bracken_build_database.py Wed Jul 31 18:08:06 2019 -0400 @@ -25,7 +25,7 @@ database_name = database_name - database_path = database_value + database_path = bracken_build_args['kraken_database'] try: os.mkdir( os.path.join(target_directory, database_path) ) @@ -35,8 +35,7 @@ else: raise - - + bracken_build_args_list = [ '-t', bracken_build_args['threads'], '-k', bracken_build_args['kmer_len'], @@ -46,12 +45,7 @@ subprocess.check_call(['bracken-build'] + bracken_build_args_list, cwd=os.path.join(target_directory, database_path)) - - bagit_args_list = [ - database_path, - ] - subprocess.call(['bagit.py'] + bagit_args_list, cwd=target_directory) data_table_entry = { "data_tables": { @@ -59,7 +53,7 @@ { "value": database_value, "name": database_name, - "path": os.path.join(database_path, 'data'), + "path": os.path.join(database_path), } ] }
--- a/data_manager_conf.xml Fri Jul 26 17:18:22 2019 -0400 +++ b/data_manager_conf.xml Wed Jul 31 18:08:06 2019 -0400 @@ -6,8 +6,8 @@ <column name="name"/> <column name="path" output_ref="out_file"> <move type="file"> - <source>#import os#${os.path.dirname($path)}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/#import os#${os.path.dirname($path)}</target> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${path}</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${path}</value_translation> <value_translation type="function">abspath</value_translation>