Mercurial > repos > recetox > msmetaenhancer

comparison msmetaenhancer_wrapper.py @ 0:053ce79ed564 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
author recetox
date Tue, 11 Jan 2022 15:12:26 +0000
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children 4ae5b466a805
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-1:000000000000 0:053ce79ed564
1 import argparse
2 import asyncio
3 import sys
4
5
6 from MSMetaEnhancer import Application
7
8
9 def main(argv):
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.")
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.")
14 args = parser.parse_args()
15
16 app = Application()
17
18 # import .msp file
19 app.load_spectra(args.input_file, file_format='msp')
20
21 # curate given metadata
22 app.curate_spectra()
23
24 # specify requested services and jobs
25 services = ['PubChem', 'CTS', 'CIR', 'NLM']
26
27 if len(args.jobs) != 0:
28 jobs = []
29 for job in args.jobs.split(","):
30 if len(job) != 0:
31 jobs.append(job.split())
32 asyncio.run(app.annotate_spectra(services, jobs))
33 else:
34 # execute without jobs parameter to run all possible jobs
35 asyncio.run(app.annotate_spectra(services))
36
37 # export .msp file
38 app.save_spectra(args.output_file, file_format="msp")
39 return 0
40
41
42 if __name__ == "__main__":
43 main(argv=sys.argv[1:])