Mercurial > repos > rv43 > tomo

comparison tomo_setup.py @ 63:98a83f03d91b draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit a9ebbfca439737ae17ddcb0df84408155f964877"
author rv43
date Thu, 18 Aug 2022 14:36:46 +0000
parents 75dd6e15f628
children ba5866d0251d
comparison
equal deleted inserted replaced
62:e544e5d110eb 63:98a83f03d91b
125 continue 125 continue
126 fields = [x.strip() for x in line.split('\t')] 126 fields = [x.strip() for x in line.split('\t')]
127 filepath = fields[0] 127 filepath = fields[0]
128 element_identifier = fields[1] if len(fields) > 1 else fields[0].split('/')[-1] 128 element_identifier = fields[1] if len(fields) > 1 else fields[0].split('/')[-1]
129 datasets.append({'element_identifier' : element_identifier, 'filepath' : filepath}) 129 datasets.append({'element_identifier' : element_identifier, 'filepath' : filepath})
130 print(f'datasets:\n{datasets}')
131 logging.debug(f'datasets:\n{datasets}') 130 logging.debug(f'datasets:\n{datasets}')
132 if input_type == 'files' and len(datasets) != num_stack: 131 if input_type == 'files' and len(datasets) != num_stack:
133 raise ValueError('Inconsistent number of input files provided.') 132 raise ValueError('Inconsistent number of input files provided.')
134 133
135 # Read and sort data files 134 # Read and sort data files
158 if len(collection): 157 if len(collection):
159 collection[0]['filepaths'].append(filepath) 158 collection[0]['filepaths'].append(filepath)
160 else: 159 else:
161 collection = {'name' : name, 'filepaths' : [filepath]} 160 collection = {'name' : name, 'filepaths' : [filepath]}
162 collections.append(collection) 161 collections.append(collection)
163 print(f'collections:\n{collections}')
164 logging.debug(f'collections:\n{collections}') 162 logging.debug(f'collections:\n{collections}')
165 163
166 # Instantiate Tomo object 164 # Instantiate Tomo object
167 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 165 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
168 log_stream=args.log, galaxy_flag=True) 166 log_stream=args.log, galaxy_flag=True)