Mercurial > repos > recetox > msmetaenhancer

comparison msmetaenhancer_wrapper.py @ 3:f387ebd6b734 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"
author recetox
date Fri, 06 May 2022 12:21:30 +0000
parents 8338640d8676
children 2ada1099f42e
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2:8338640d8676 3:f387ebd6b734
10 parser = argparse.ArgumentParser(description="Annotate MSP file.") 10 parser = argparse.ArgumentParser(description="Annotate MSP file.")
11 parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.") 11 parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
12 parser.add_argument("--output_file", type=str, help="Path to output spectra file.") 12 parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
13 parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.") 13 parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
14 parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.") 14 parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
15 parser.add_argument("--log_level", type=str, default='info',
16 help="Severity of log messages present in the log file.")
15 args = parser.parse_args() 17 args = parser.parse_args()
16 18
17 app = Application(log_file=args.log_file) 19 app = Application(log_level=args.log_level, log_file=args.log_file)
18 20
19 # set matchms logging level to avoid extensive messages in stdout while reading file 21 # set matchms logging level to avoid extensive messages in stdout while reading file
20 set_matchms_logger_level("ERROR") 22 set_matchms_logger_level("ERROR")
21 # import .msp file 23 # import .msp file
22 app.load_spectra(args.input_file, file_format='msp') 24 app.load_spectra(args.input_file, file_format='msp')