comparison msmetaenhancer_wrapper.py @ 2:8338640d8676 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit fc4fc95ed79d03b2f8d075d0df27d75eb93c58ea"

1:b50c2e941cae

import argparse
import asyncio
import sys


from MSMetaEnhancer import Application


def main(argv):
    parser = argparse.ArgumentParser(description="Annotate MSP file.")

    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
    args = parser.parse_args()

    app = Application(log_file=args.log_file)

    # import .msp file
    app.load_spectra(args.input_file, file_format='msp')

    # curate given metadata
    app.curate_spectra()

    # specify requested services and jobs

2:8338640d8676

import argparse
import asyncio
import sys

from matchms import set_matchms_logger_level
from MSMetaEnhancer import Application


def main(argv):
    parser = argparse.ArgumentParser(description="Annotate MSP file.")

    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
    args = parser.parse_args()

    app = Application(log_file=args.log_file)

    # set matchms logging level to avoid extensive messages in stdout while reading file
    set_matchms_logger_level("ERROR")
    # import .msp file
    app.load_spectra(args.input_file, file_format='msp')

    # set matchms logging level back to warning
    set_matchms_logger_level("WARNING")

    # curate given metadata
    app.curate_spectra()

    # specify requested services and jobs