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comparison tomo_setup.py @ 53:d34915cfd997 draft

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"planemo upload for repository https://github.com/rolfverberg/galaxytools commit db0affe73093d1bf862c83aad93b375374a7ee11"
author rv43
date Thu, 28 Jul 2022 17:26:54 +0000
parents 1c7f86ab84aa
children 71aea0636efe
comparison
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52:1c7f86ab84aa 53:d34915cfd997
66 66
67 # Check input file type 67 # Check input file type
68 print(f'inputfiles ({type(args.inputfiles)}):\n{args.inputfiles}') 68 print(f'inputfiles ({type(args.inputfiles)}):\n{args.inputfiles}')
69 print(f'inputfile_types ({type(args.inputfile_types)}):\n{args.inputfile_types}') 69 print(f'inputfile_types ({type(args.inputfile_types)}):\n{args.inputfile_types}')
70 if isinstance(args.inputfile_types, list): 70 if isinstance(args.inputfile_types, list):
71 if args.inputfile_types[0] == 'collection': 71 if if len(args.inputfile_types) == 1 and args.inputfile_types[0] == 'collection':
72 input_as_collection = True 72 if len(args.inputfiles) != 1 or args.inputfiles[0] != 'inputfiles.txt':
73 if len(args.inputfiles) != 1 or args.inputfiles[0] != inputfiles.txt:
74 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+ 73 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+
75 f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+ 74 f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+
76 f'inputfile_types ({type(inputfile_types)}):\n{inputfile_types}') 75 f'inputfile_types ({type(inputfile_types)}):\n{inputfile_types}')
76 input_as_collection = True
77 else: 77 else:
78 if len(args.inputfiles) != len(args.inputfile_types):
79 raise ValueError('Inconsistent inputfiles and inputfile_types:\n'+
80 f'inputfiles ({type(inputfiles)}):\n{inputfiles}\n'+
81 f'inputfile_types ({type(inputfile_types)}):\n{inputfile_types}')
78 input_as_collection = False 82 input_as_collection = False
79 else: 83 else:
80 raise ValueError(f'Invalid args.inputfile_types: {args.inputfile_types} '+ 84 raise ValueError(f'Invalid args.inputfile_types: {args.inputfile_types} '+
81 f'{type(args.inputfile_types)}') 85 f'{type(args.inputfile_types)}')
82 86
83 datasets = [] 87 datasets = []
84 collections = [] 88 collections = []
85 if input_as_collection: 89 if input_as_collection:
86 # Read input file collections and collect data files info 90 # Read input file collections and collect data files info
87 with open(args.inputfiles) as cf: 91 with open(args.inputfiles[0]) as cf:
88 for line in cf: 92 for line in cf:
89 if not line.strip() or line.startswith('#'): 93 if not line.strip() or line.startswith('#'):
90 continue 94 continue
91 fields = [x.strip() for x in line.split('\t')] 95 fields = [x.strip() for x in line.split('\t')]
92 filepath = fields[0] 96 filepath = fields[0]