Mercurial > repos > rv43 > tomo

comparison tomo_setup.py @ 55:bead50a4eadc draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit 0b92f646a095298322c09fd2731602fa8994f76c"
author rv43
date Thu, 28 Jul 2022 17:44:49 +0000
parents 71aea0636efe
children feb2a5fc7c76
comparison
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54:71aea0636efe 55:bead50a4eadc
63 logging.debug(f'output_config = {args.output_config}') 63 logging.debug(f'output_config = {args.output_config}')
64 logging.debug(f'output_data = {args.output_data}') 64 logging.debug(f'output_data = {args.output_data}')
65 logging.debug(f'tomoranges = {args.tomo_ranges}') 65 logging.debug(f'tomoranges = {args.tomo_ranges}')
66 66
67 # Check input file type 67 # Check input file type
68 print(f'inputfiles ({type(args.inputfiles)}):\n{args.inputfiles}')
69 print(f'inputfile_types ({type(args.inputfile_types)}):\n{args.inputfile_types}')
70 if isinstance(args.inputfile_types, list): 68 if isinstance(args.inputfile_types, list):
71 if len(args.inputfile_types) == 1 and args.inputfile_types[0] == 'collection': 69 if len(args.inputfile_types) == 1 and args.inputfile_types[0] == 'collection':
72 if len(args.inputfiles) != 1 or args.inputfiles[0] != 'inputfiles.txt': 70 if len(args.inputfiles) != 1 or args.inputfiles[0] != 'inputfiles.txt':
73 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+ 71 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+
74 f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+ 72 f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+
119 # Collect input file datasets info 117 # Collect input file datasets info
120 collections = [{'name' : filetype, 'filepaths' : [filepath]} 118 collections = [{'name' : filetype, 'filepaths' : [filepath]}
121 for filetype, filepath in zip(args.inputfile_types, args.inputfiles)] 119 for filetype, filepath in zip(args.inputfile_types, args.inputfiles)]
122 logging.debug(f'collections:\n{collections}') 120 logging.debug(f'collections:\n{collections}')
123 if len(args.tomo_ranges) != 2*len(collections): 121 if len(args.tomo_ranges) != 2*len(collections):
124 print(f'datasets ({type(datasets)} {len(datasets)}):\n{datasets}')
125 print(f'collections ({type(collections)} {len(collections)}):\n{collections}')
126 print(f'ranges ({type(args.tomo_ranges)} {len(args.tomo_ranges)}):\n{args.tomo_ranges}')
127 raise ValueError('Inconsistent tomo ranges size.') 122 raise ValueError('Inconsistent tomo ranges size.')
128 123
129 # Instantiate Tomo object 124 # Instantiate Tomo object
130 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level, 125 tomo = Tomo(config_file=args.config, config_out=args.output_config, log_level=log_level,
131 log_stream=args.log, galaxy_flag=True) 126 log_stream=args.log, galaxy_flag=True)