Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
changeset 17:db293ee25be5 draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 0745f158bbb0d5d190cc4503157d2d3092ab8cc5
| author | sanbi-uwc |
|---|---|
| date | Fri, 15 Apr 2016 09:03:40 -0400 |
| parents | 6437b3c7bb84 |
| children | 2b89ba1c0057 |
| files | data_manager/novocraft_index_builder.py data_manager/novocraft_index_builder.xml |
| diffstat | 2 files changed, 12 insertions(+), 29 deletions(-) [+] |
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--- a/data_manager/novocraft_index_builder.py Thu Mar 31 09:57:08 2016 -0400 +++ b/data_manager/novocraft_index_builder.py Fri Apr 15 09:03:40 2016 -0400 @@ -17,20 +17,14 @@ DEFAULT_DATA_TABLE_NAME = "novocraft_index" def get_dbkey_id_name(params, dbkey_description=None): - dbkey = params['param_dict']['dbkey'] # TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] - if not sequence_id: - sequence_id = dbkey # uuid.uuid4() generate and use an uuid instead? - sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = dbkey_description - if not sequence_name: - sequence_name = dbkey - return dbkey, sequence_id, sequence_name + return sequence_id, sequence_name -def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, add_system_module, data_table_name=DEFAULT_DATA_TABLE_NAME): +def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME): if os.path.exists(target_directory) and not os.path.isdir(target_directory): print("Output directory path already exists but is not a directory: {}".format(target_directory), file=sys.stderr) @@ -43,13 +37,11 @@ cmdline = shlex.split(cmdline_str) try: - if add_system_module == 'true': - check_call(['module add novoindex']) check_call(cmdline) except CalledProcessError: print("Error building RNA STAR index", file=sys.stderr) - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename ) + data_table_entry = dict( value=sequence_id, dbkey=sequence_id, name=sequence_name, path=index_filename ) _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): @@ -58,18 +50,18 @@ data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) return data_manager_dict -def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, add_system_module, data_table_name=DEFAULT_DATA_TABLE_NAME ): +def download_from_url( data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): # TODO: we should automatically do decompression here urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n'))) fasta_reader = [urllib2.urlopen(url) for url in urls] - _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, dbkey, sequence_id, sequence_name, data_table_name, add_system_module) + _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, sequence_id, sequence_name, data_table_name) -def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, add_system_module, data_table_name=DEFAULT_DATA_TABLE_NAME ): +def download_from_history( data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): # TODO: allow multiple FASTA input files input_filename = params['param_dict']['reference_source']['input_fasta'] - _make_novocraft_index(data_manager_dict, input_filename, target_directory, dbkey, sequence_id, sequence_name, add_system_module, data_table_name ) + _make_novocraft_index(data_manager_dict, input_filename, target_directory, sequence_id, sequence_name, data_table_name ) REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history) @@ -78,7 +70,6 @@ parser.add_argument('output_filename') parser.add_argument('--dbkey_description') parser.add_argument('--data_table_name', default='novocraft_index') - parser.add_argument('--add_system_module', default=False) args = parser.parse_args() filename = args.output_filename @@ -88,14 +79,11 @@ os.makedirs(target_directory) data_manager_dict = {} - dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) - - if dbkey in [None, '', '?']: - raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) + sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) # Fetch the FASTA REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\ - (data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name, args.add_system_module, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME ) + (data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME ) open(filename, 'wb').write(dumps( data_manager_dict ))
--- a/data_manager/novocraft_index_builder.xml Thu Mar 31 09:57:08 2016 -0400 +++ b/data_manager/novocraft_index_builder.xml Fri Apr 15 09:03:40 2016 -0400 @@ -1,21 +1,17 @@ <?xml version="1.0" encoding="utf-8" ?> <tool id="novocraft_index_builder" name="NOVO CRAFT index" tool_type="manage_data" version="0.0.1"> <description>Build an index for use by the Novo Craft mapping tool</description> - <requirements> - <requirement type="package" version="3.04.01">novocraft</requirement> - </requirements> <stdio> <exit_code range=":-1" /> <exit_code range="1:" /> </stdio> <command interpreter="python"> - novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index" --add_system_module ${add_system_module} + novocraft_index_builder.py "${out_file}" --data_table_name "novocraft_index" </command> <inputs> - <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> - <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_name" value="" label="Name of sequence" optional="False" /> <param type="text" name="sequence_desc" value="" label="Description of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" optional="False" /> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="url">URL</option> @@ -28,7 +24,6 @@ <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> </when> </conditional> - <param name="add_system_module" type="boolean" label="Add a Novo-align system Module" checked="true" truevalue="true" value="false" help="Add novoindex system module"/> </inputs> <outputs> <data name="out_file" format="data_manager_json" />