@cli.command()<EOL>@click.option('<STR_LIT>', '<STR_LIT>', required=True, type=click.Path(exists=True), help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', '<STR_LIT>', type=click.Path(exists=False), help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=True, show_default=True, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=True, show_default=True, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=True, show_default=True, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=False, show_default=True, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=<NUM_LIT>, show_default=True, type=float, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=<NUM_LIT>, show_default=True, type=float, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=<NUM_LIT>, show_default=True, type=float, help='<STR_LIT>')<EOL>@click.option('<STR_LIT>', default=<NUM_LIT>, show_default=True, type=float, help='<STR_LIT>')<EOL>def ipf(infile, outfile, ipf_ms1_scoring, ipf_ms2_scoring, ipf_h0, ipf_grouped_fdr, ipf_max_precursor_pep, ipf_max_peakgroup_pep, ipf_max_precursor_peakgroup_pep, ipf_max_transition_pep):
if outfile is None:<EOL><INDENT>outfile = infile<EOL><DEDENT>else:<EOL><INDENT>outfile = outfile<EOL><DEDENT>infer_peptidoforms(infile, outfile, ipf_ms1_scoring, ipf_ms2_scoring, ipf_h0, ipf_grouped_fdr, ipf_max_precursor_pep, ipf_max_peakgroup_pep, ipf_max_precursor_peakgroup_pep, ipf_max_transition_pep)<EOL>
Infer peptidoforms after scoring of MS1, MS2 and transition-level data.