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comparison workflow/link_to_galaxy.py @ 71:1cf15b61cd83 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213
author rv43
date Mon, 20 Mar 2023 13:56:57 +0000
parents fba792d5f83b
children
comparison
equal deleted inserted replaced
70:97c4e2cbbad9 71:1cf15b61cd83
35 return (library_id, folder_id, new_folders) 35 return (library_id, folder_id, new_folders)
36 36
37 def link_to_galaxy(filename:str, galaxy=None, user=None, password=None, api_key=None) -> None: 37 def link_to_galaxy(filename:str, galaxy=None, user=None, password=None, api_key=None) -> None:
38 # Read input file 38 # Read input file
39 extension = path.splitext(filename)[1] 39 extension = path.splitext(filename)[1]
40 if extension == '.yml' or extension == '.yaml': 40 # RV yaml input not incorporated yet, since Galaxy can't use pyspec right now
41 with open(filename, 'r') as f: 41 # if extension == '.yml' or extension == '.yaml':
42 data = safe_load(f) 42 # with open(filename, 'r') as f:
43 elif extension == '.nxs': 43 # data = safe_load(f)
44 # elif extension == '.nxs':
45 if extension == '.nxs':
44 with NXFile(filename, mode='r') as nxfile: 46 with NXFile(filename, mode='r') as nxfile:
45 data = nxfile.readfile() 47 data = nxfile.readfile()
46 else: 48 else:
47 raise ValueError(f'Invalid filename extension ({extension})') 49 raise ValueError(f'Invalid filename extension ({extension})')
48 if isinstance(data, dict): 50 if isinstance(data, dict):
51 if len(wf.sample_maps) > 1: 53 if len(wf.sample_maps) > 1:
52 raise ValueError(f'Multiple sample maps not yet implemented') 54 raise ValueError(f'Multiple sample maps not yet implemented')
53 nxroot = NXroot() 55 nxroot = NXroot()
54 for sample_map in wf.sample_maps: 56 for sample_map in wf.sample_maps:
55 import_scanparser(sample_map.station) 57 import_scanparser(sample_map.station)
56 sample_map.construct_nxentry(nxroot, include_raw_data=False) 58 # RV raw data must be included, since Galaxy can't use pyspec right now
59 # sample_map.construct_nxentry(nxroot, include_raw_data=False)
60 sample_map.construct_nxentry(nxroot, include_raw_data=True)
57 nxentry = nxroot[nxroot.attrs['default']] 61 nxentry = nxroot[nxroot.attrs['default']]
58 elif isinstance(data, NXroot): 62 elif isinstance(data, NXroot):
59 nxentry = data[data.attrs['default']] 63 nxentry = data[data.attrs['default']]
60 else: 64 else:
61 raise ValueError(f'Invalid input file data ({data})') 65 raise ValueError(f'Invalid input file data ({data})')