Mercurial > repos > dfornika > mentalist
changeset 24:e038a8823a99 draft
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty
| author | dfornika |
|---|---|
| date | Thu, 12 Oct 2017 15:19:43 -0400 |
| parents | d151478ebf97 |
| children | b9dfa8aa503d |
| files | data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py |
| diffstat | 3 files changed, 12 insertions(+), 10 deletions(-) [+] |
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--- a/data_managers/data_manager_conf.xml Thu Oct 12 13:40:07 2017 -0400 +++ b/data_managers/data_manager_conf.xml Thu Oct 12 15:19:43 2017 -0400 @@ -9,7 +9,7 @@ <move type="directory" relativize_symlinks="True"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -24,7 +24,7 @@ <move type="directory" relativize_symlinks="True"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -39,7 +39,7 @@ <move type="directory" relativize_symlinks="True"> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Thu Oct 12 13:40:07 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Thu Oct 12 15:19:43 2017 -0400 @@ -16,17 +16,19 @@ def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): - scheme_files_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_cgmlst" - database_path = scheme_files_path + "_k" + str(kmer_size) - database_name = database_path + ".h5" - display_name = scheme + " k=" + str(kmer_size) + " (cgMLST)" - args = [ 'mentalist', 'download_cgmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o', scheme_files_path] + translation_table = string.maketrans(string.punctuation, ("_" * 32)) + base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst" + scheme_files_path = base_path + "_scheme" + database_path = base_path + "_k" + str(kmer_size) + database_name = base_path + "_k" + str(kmer_size) + ".h5" + display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)" + args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait() if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - data_table_entry = dict( value=database_name, dbkey='cgMLST', name=display_name, path=(database_path + "/" + database_name) ) + data_table_entry = dict( value=database_path, dbkey='cgMLST', name=display_name, path=database_name ) for data_table_name in data_table_names: _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Thu Oct 12 13:40:07 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Thu Oct 12 15:19:43 2017 -0400 @@ -28,7 +28,7 @@ if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=(database_path + "/" + database_name) ) + data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=database_name ) for data_table_name in data_table_names: _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )