from glycoprophet.plot import export_peakgroup_plots
import click


@click.command()
@click.option('--in', 'osw_file', required=True, type=click.Path(exists=
    True), help='Input OSW file.')
@click.option('--mzml', 'mzml_file', required=True, type=click.Path(exists=
    True), help='Input mzML file.')
@click.option('--swath_windows', 'swath_window_file', type=click.Path(
    exists=True), help='SWATH window file (TSV).')
@click.option('--transition_groups', 'transition_group_file', type=click.
    Path(exists=True), help='Transition group-level result file (TSV).')
@click.option('--glycoform/--no-glycoform', 'glycoform', default=False,
    show_default=True, help='Export glycoform results.')
@click.option('--max_peakgroup_rank', default=1, show_default=True, type=
    int, help=
    'Filter results to candidate peak groups until maximum peak group rank.')
@click.option('--max_rs_peakgroup_qvalue', default=0.05, show_default=True,
    type=float, help=
    'Filter results to maximum run-specific peak group-level q-value.')
@click.option('--max_glycoform_qvalue', default=0.05, show_default=True,
    type=float, help='Filter results to maximum glycoform q-value.')
@click.option('--include_decoy/--exclude_decoy', 'include_decoy', default=
    False, show_default=True, help='Include decoy results.')
@click.option('--tolerance', default=20, show_default=True, type=float,
    help='m/z extraction window.')
@click.option('--tolerance_unit', default='ppm', show_default=True, type=
    click.Choice(['ppm', 'Da']), help='m/z extraction window unit.')
def export_plots(osw_file, mzml_file, swath_window_file,
    transition_group_file, glycoform, max_peakgroup_rank,
    max_rs_peakgroup_qvalue, max_glycoform_qvalue, include_decoy, tolerance,
    tolerance_unit):
    """
    Export peak group plots
    """
    export_peakgroup_plots(osw_file=osw_file, mzml_file=mzml_file,
        swath_window_file=swath_window_file, transition_group_file=
        transition_group_file, glycoform=glycoform, max_peakgroup_rank=
        max_peakgroup_rank, max_rs_peakgroup_qvalue=max_rs_peakgroup_qvalue,
        max_glycoform_qvalue=max_glycoform_qvalue, include_decoy=
        include_decoy, tolerance=tolerance, tolerance_unit=tolerance_unit)


if __name__ == '__main__':
    export_plots()

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@click.command()
@click.option('--in', 'osw_file', required=True, type=click.Path(exists=
    True), help='Input OSW file.')
@click.option('--mzml', 'mzml_file', required=True, type=click.Path(exists=
    True), help='Input mzML file.')
@click.option('--swath_windows', 'swath_window_file', type=click.Path(
    exists=True), help='SWATH window file (TSV).')
@click.option('--transition_groups', 'transition_group_file', type=click.
    Path(exists=True), help='Transition group-level result file (TSV).')
@click.option('--glycoform/--no-glycoform', 'glycoform', default=False,
    show_default=True, help='Export glycoform results.')
@click.option('--max_peakgroup_rank', default=1, show_default=True, type=
    int, help=
    'Filter results to candidate peak groups until maximum peak group rank.')
@click.option('--max_rs_peakgroup_qvalue', default=0.05, show_default=True,
    type=float, help=
    'Filter results to maximum run-specific peak group-level q-value.')
@click.option('--max_glycoform_qvalue', default=0.05, show_default=True,
    type=float, help='Filter results to maximum glycoform q-value.')
@click.option('--include_decoy/--exclude_decoy', 'include_decoy', default=
    False, show_default=True, help='Include decoy results.')
@click.option('--tolerance', default=20, show_default=True, type=float,
    help='m/z extraction window.')
@click.option('--tolerance_unit', default='ppm', show_default=True, type=
    click.Choice(['ppm', 'Da']), help='m/z extraction window unit.')
def export_plots(osw_file, mzml_file, swath_window_file,
    transition_group_file, glycoform, max_peakgroup_rank,
    max_rs_peakgroup_qvalue, max_glycoform_qvalue, include_decoy, tolerance,
    tolerance_unit):
    """
    Export peak group plots
    """
    export_peakgroup_plots(osw_file=osw_file, mzml_file=mzml_file,
        swath_window_file=swath_window_file, transition_group_file=
        transition_group_file, glycoform=glycoform, max_peakgroup_rank=
        max_peakgroup_rank, max_rs_peakgroup_qvalue=max_rs_peakgroup_qvalue,
        max_glycoform_qvalue=max_glycoform_qvalue, include_decoy=
        include_decoy, tolerance=tolerance, tolerance_unit=tolerance_unit)


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@click.command()
@click.option('--in', 'osw_file', required=True, type=click.Path(exists=
    True), help='Input OSW file.')
@click.option('--mzml', 'mzml_file', required=True, type=click.Path(exists=
    True), help='Input mzML file.')
@click.option('--swath_windows', 'swath_window_file', type=click.Path(
    exists=True), help='SWATH window file (TSV).')
@click.option('--transition_groups', 'transition_group_file', type=click.
    Path(exists=True), help='Transition group-level result file (TSV).')
@click.option('--glycoform/--no-glycoform', 'glycoform', default=False,
    show_default=True, help='Export glycoform results.')
@click.option('--max_peakgroup_rank', default=1, show_default=True, type=
    int, help=
    'Filter results to candidate peak groups until maximum peak group rank.')
@click.option('--max_rs_peakgroup_qvalue', default=0.05, show_default=True,
    type=float, help=
    'Filter results to maximum run-specific peak group-level q-value.')
@click.option('--max_glycoform_qvalue', default=0.05, show_default=True,
    type=float, help='Filter results to maximum glycoform q-value.')
@click.option('--include_decoy/--exclude_decoy', 'include_decoy', default=
    False, show_default=True, help='Include decoy results.')
@click.option('--tolerance', default=20, show_default=True, type=float,
    help='m/z extraction window.')
@click.option('--tolerance_unit', default='ppm', show_default=True, type=
    click.Choice(['ppm', 'Da']), help='m/z extraction window unit.')
def export_plots(osw_file, mzml_file, swath_window_file,
    transition_group_file, glycoform, max_peakgroup_rank,
    max_rs_peakgroup_qvalue, max_glycoform_qvalue, include_decoy, tolerance,
    tolerance_unit):
    """
    Export peak group plots
    """
    export_peakgroup_plots(osw_file=osw_file, mzml_file=mzml_file,
        swath_window_file=swath_window_file, transition_group_file=
        transition_group_file, glycoform=glycoform, max_peakgroup_rank=
        max_peakgroup_rank, max_rs_peakgroup_qvalue=max_rs_peakgroup_qvalue,
        max_glycoform_qvalue=max_glycoform_qvalue, include_decoy=
        include_decoy, tolerance=tolerance, tolerance_unit=tolerance_unit)


if __name__ == '__main__':
    export_plots()

from glycoprophet.plot import export_peakgroup_plots
import click


@click.command()
@click.option('--in', 'osw_file', required=True, type=click.Path(exists=
    True), help='Input OSW file.')
@click.option('--mzml', 'mzml_file', required=True, type=click.Path(exists=
    True), help='Input mzML file.')
@click.option('--swath_windows', 'swath_window_file', type=click.Path(
    exists=True), help='SWATH window file (TSV).')
@click.option('--transition_groups', 'transition_group_file', type=click.
    Path(exists=True), help='Transition group-level result file (TSV).')
@click.option('--glycoform/--no-glycoform', 'glycoform', default=False,
    show_default=True, help='Export glycoform results.')
@click.option('--max_peakgroup_rank', default=1, show_default=True, type=
    int, help=
    'Filter results to candidate peak groups until maximum peak group rank.')
@click.option('--max_rs_peakgroup_qvalue', default=0.05, show_default=True,
    type=float, help=
    'Filter results to maximum run-specific peak group-level q-value.')
@click.option('--max_glycoform_qvalue', default=0.05, show_default=True,
    type=float, help='Filter results to maximum glycoform q-value.')
@click.option('--include_decoy/--exclude_decoy', 'include_decoy', default=
    False, show_default=True, help='Include decoy results.')
@click.option('--tolerance', default=20, show_default=True, type=float,
    help='m/z extraction window.')
@click.option('--tolerance_unit', default='ppm', show_default=True, type=
    click.Choice(['ppm', 'Da']), help='m/z extraction window unit.')
def export_plots(osw_file, mzml_file, swath_window_file,
    transition_group_file, glycoform, max_peakgroup_rank,
    max_rs_peakgroup_qvalue, max_glycoform_qvalue, include_decoy, tolerance,
    tolerance_unit):
    """
    Export peak group plots
    """
    export_peakgroup_plots(osw_file=osw_file, mzml_file=mzml_file,
        swath_window_file=swath_window_file, transition_group_file=
        transition_group_file, glycoform=glycoform, max_peakgroup_rank=
        max_peakgroup_rank, max_rs_peakgroup_qvalue=max_rs_peakgroup_qvalue,
        max_glycoform_qvalue=max_glycoform_qvalue, include_decoy=
        include_decoy, tolerance=tolerance, tolerance_unit=tolerance_unit)


if __name__ == '__main__':
    export_plots()
