comparison matchms_filtering_wrapper.py @ 17:7627b40601f6 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8db07edd3b0d2ff778036dec410027ad58365488

16:26c92af1bd28

import argparse
import sys

from matchms.exporting import save_as_mgf, save_as_msp
from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz, \
    add_retention_index, add_retention_time, clean_compound_name
from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
    select_by_relative_intensity
from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass
from matchms.importing import load_from_mgf, load_from_msp

    parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
    parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")
    parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
    parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
    parser.add_argument("-normalise_intensities", action='store_true',
                        help="Normalize intensities of peaks (and losses) to unit height.")
    parser.add_argument("-default_filters", action='store_true',
                        help="Collection of filters that are considered default and that do no require any (factory) arguments.")
    parser.add_argument("-clean_metadata", action='store_true',
                        help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.")
    parser.add_argument("-relative_intensity", action='store_true',

        if args.default_filters:
            spectrum = default_filters(spectrum)

        if args.clean_metadata:
            filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass,
                       add_retention_index, add_retention_time, clean_compound_name]
            for metadata_filter in filters:
                spectrum = metadata_filter(spectrum)

        if args.relative_intensity:

17:7627b40601f6

import argparse
import sys

from matchms.exporting import save_as_mgf, save_as_msp
from matchms.filtering import add_compound_name, add_fingerprint, add_parent_mass, add_precursor_mz, \
    add_retention_index, add_retention_time, clean_compound_name
from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
    select_by_relative_intensity
from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass
from matchms.importing import load_from_mgf, load_from_msp

    parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
    parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")
    parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
    parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
    parser.add_argument("-normalise_intensities", action='store_true',
                        help="Normalize intensities of peaks to unit height.")
    parser.add_argument("-default_filters", action='store_true',
                        help="Collection of filters that are considered default and that do no require any (factory) arguments.")
    parser.add_argument("-clean_metadata", action='store_true',
                        help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.")
    parser.add_argument("-relative_intensity", action='store_true',

        if args.default_filters:
            spectrum = default_filters(spectrum)

        if args.clean_metadata:
            filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_parent_mass,
                       add_retention_index, add_retention_time, clean_compound_name]
            for metadata_filter in filters:
                spectrum = metadata_filter(spectrum)

        if args.relative_intensity: