Mercurial > repos > jjohnson > eggnog_mapper
changeset 3:9d94fe7ce8b9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit e711920c41c8862d7d8133f7b455cf475924e103
| author | jjohnson |
|---|---|
| date | Tue, 05 Nov 2019 15:53:42 -0500 |
| parents | a74d61dbd155 |
| children | ea9772670fb5 |
| files | data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml data_manager_conf.xml |
| diffstat | 3 files changed, 37 insertions(+), 24 deletions(-) [+] |
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--- a/data_manager/data_manager_eggnog.py Mon Nov 04 16:38:44 2019 -0500 +++ b/data_manager/data_manager_eggnog.py Tue Nov 05 15:53:42 2019 -0500 @@ -6,8 +6,9 @@ import json import os.path import sqlite3 +import sys from sqlite3 import OperationalError -import sys + def _get_db_version(sqlitedb_path): version = '4.5' @@ -18,40 +19,47 @@ cur.execute(query) version = cur.fetchone()[0] except OperationalError as e: - print('Assuming eggnog version %s because %s %s' % (version, sqlitedb_path, e), file=sys.stderr) + print('Assuming eggnog version %s because %s %s' % + (version, sqlitedb_path, e), file=sys.stderr) return version + def main(): parser = argparse.ArgumentParser() - parser.add_argument( '--config_file' ) - parser.add_argument( '--install_path' ) - parser.add_argument( '--dbs', default='') + parser.add_argument('--config_file') + parser.add_argument('--install_path') + parser.add_argument('--dbs', default='') args = parser.parse_args() - eggnog_db_path = os.path.join(args.install_path,'eggnog.db') + eggnog_db_path = os.path.join(args.install_path, 'eggnog.db') if not os.path.exists(eggnog_db_path): print('Can not open: %s' % eggnog_db_path, file=sys.stderr) exit(1) db_version = _get_db_version(eggnog_db_path) - params = json.loads( open( args.config_file ).read() ) - data_manager_dict = {} - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + # params = json.loads(open(args.config_file).read()) + dm_dict = {} + dm_dict['data_tables'] = dm_dict.get('data_tables', {}) data_table = 'eggnog_mapper_db' - data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) - data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path) - data_manager_dict['data_tables'][data_table].append( data_table_entry ) + dm_dict['data_tables'][data_table]\ + = dm_dict['data_tables'].get(data_table, []) + data_table_entry = dict(value=db_version, name=db_version, + path=eggnog_db_path) + dm_dict['data_tables'][data_table].append(data_table_entry) data_table = 'eggnog_mapper_hmm_dbs' - data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) + dm_dict['data_tables'][data_table]\ + = dm_dict['data_tables'].get(data_table, []) if args.dbs: dbs = [x.strip() for x in args.dbs.split(',')] for db in dbs: key = '%s_%s' % (db_version, db) - data_table_entry = dict(key=key, db_version=db_version, value=db, name=db, path=db) - data_manager_dict['data_tables'][data_table].append( data_table_entry ) + data_table_entry = dict(key=key, db_version=db_version, + value=db, name=db, path=db) + dm_dict['data_tables'][data_table].append(data_table_entry) # save info to json file - open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) ) + open(args.config_file, 'wb').write(json.dumps(dm_dict)) + if __name__ == "__main__": main()
--- a/data_manager/data_manager_eggnog.xml Mon Nov 04 16:38:44 2019 -0500 +++ b/data_manager/data_manager_eggnog.xml Tue Nov 05 15:53:42 2019 -0500 @@ -1,7 +1,7 @@ -<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data"> +<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@.0" tool_type="manage_data"> <description>Download a new database</description> <macros> - <token name="@VERSION@">4.5.1</token> + <token name="@VERSION@">1.0.3</token> </macros> <requirements> <requirement type="package" version="@VERSION@">eggnog-mapper</requirement> @@ -12,17 +12,19 @@ #set params = json.loads(open(str($out_file)).read()) #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') #if $dbs: -#set $eggnogdbs = ' '.join($dbs.split(',')) +#set $eggnogdbs = ' '.join(str($dbs).split(',')) #else #set $eggnogdbs = 'none' -#endif +#end if #if $test == 'false' -mkdir -p '${target_directory}' && +mkdir -p '${install_path}' && download_eggnog_data.py $diamond_database -y -q --data_dir $install_path $eggnogdbs ' '.join(dbs.split(',')) && +#else +#set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally' #end if -python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs' +python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs' ]]></command> <inputs> <param name="test" type="hidden" value="false" /> @@ -158,6 +160,9 @@ <help><![CDATA[ This tool downloads eggnog data using download_eggnog_data.py and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs. +The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/ +The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/ +can vary from 1G to 80G in size. ]]></help> <citations> <citation type="doi">10.1093/nar/gkv1248</citation>
--- a/data_manager_conf.xml Mon Nov 04 16:38:44 2019 -0500 +++ b/data_manager_conf.xml Tue Nov 05 15:53:42 2019 -0500 @@ -7,9 +7,9 @@ <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">eggnog_data/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/eggnog_data/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>