Mercurial > repos > recetox > msmetaenhancer
comparison msmetaenhancer_wrapper.py @ 2:4ae5b466a805 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit f09a5b3ee451d78dc025baee5eccb099f71be2b4"
| author | recetox |
|---|---|
| date | Tue, 15 Feb 2022 12:26:04 +0000 |
| parents | 053ce79ed564 |
| children | b48c57453a25 |
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| 1:4c328e0e59ab | 2:4ae5b466a805 |
|---|---|
| 9 def main(argv): | 9 def main(argv): |
| 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 args = parser.parse_args() | 15 args = parser.parse_args() |
| 15 | 16 |
| 16 app = Application() | 17 app = Application(log_file=args.log_file) |
| 17 | 18 |
| 18 # import .msp file | 19 # import .msp file |
| 19 app.load_spectra(args.input_file, file_format='msp') | 20 app.load_spectra(args.input_file, file_format='msp') |
| 20 | 21 |
| 21 # curate given metadata | 22 # curate given metadata |