parameter-names.json

{
    "_comment": "Display names for the TOPP parameters the Describe experiment page shows, per tool: \"<Tool>\": {\"<parameter path>\": \"Name\"} or {\"name\": ..., \"help\": ...}. Without \"help\" the tool's description is shown. A section path (\"SD\") names that section's heading. Parameters and sections without an entry keep the tool's name. See src/workflow/parameter_names.py.",
    "FLASHDeconv": {
        "FD": "Deconvolution",
        "SD": "Masses and charges",
        "ft": "Feature tracing",
        "iq": "Isobaric quantification",
        "keep_empty_out": "Keep empty output files",
        "write_detail": "Write peak details",
        "FD:report_FDR": {
            "name": "Estimate mass FDR (q-values)",
            "help": "Report a q-value (approximate FDR) for every deconvolved mass, with the decoy masses it was estimated from."
        },
        "FD:merging_method": "Merge spectra before deconvolution",
        "FD:merging_min_ms_level": "Merge from MS level",
        "FD:merging_max_ms_level": "Merge up to MS level",
        "FD:scan_commands": "FLASHIda scan commands file",
        "SD:tol": {
            "name": "Mass tolerance (ppm) per MS level",
            "help": "Tolerance in ppm for MS1, MS2, and so on, one value per line (e.g. 10 for MS1, then 10 for MS2)."
        },
        "SD:min_mass": "Minimum mass (Da)",
        "SD:max_mass": "Maximum mass (Da)",
        "SD:min_charge": "Minimum charge",
        "SD:max_charge": "Maximum charge",
        "SD:precursor_charge": {
            "name": "Fixed precursor charge",
            "help": "Charge of the targeted precursor: every MS2 precursor gets this charge. 0 determines the charge from the data."
        },
        "ft:ion_mobility_tolerance": "Ion mobility tolerance (1/K0)",
        "ft:min_sample_rate": "Minimum fraction of scans with signal",
        "ft:min_trace_length": "Minimum feature length (s)",
        "ft:min_cos": "Minimum isotope cosine of features",
        "ft:iso_merge_tol_ppm": "Isotope merge tolerance (ppm)",
        "iq:isotope_correction": "Correct reporter isotope impurities",
        "iq:reporter_mz_tol": "Reporter ion tolerance (Th)",
        "iq:only_fully_quantified": "Only spectra with every channel quantified"
    },
    "FLASHTnT": {
        "raw": "Spectrum matching",
        "tag": "Sequence tags",
        "ex": "Proteoform extension",
        "fixed_mod": "Fixed modifications",
        "var_mod": "Variable modifications",
        "max_var_mod_count": "Maximum variable modifications",
        "max_blind_mod_count": {
            "name": "Maximum unknown modifications",
            "help": "Maximum number of blind modifications (mass shifts not given as a modification) per proteoform."
        },
        "max_mod_mass": "Maximum unknown modification mass (Da)",
        "pro_fdr": "Proteoform FDR",
        "discard_underdetermined": "Discard underdetermined proteoforms",
        "keep_decoy": "Report decoy hits",
        "protein_level_only": "Protein-level search only",
        "ion_type": "Fragment ion types",
        "peff_max_mods": "Annotated modifications per entry (PEFF)",
        "peff_mod_masses": "Modification masses (PEFF)",
        "gapped_tags": "Candidates from gapped tags",
        "terminal_ladders": "Candidates from terminal ladders",
        "precursor_ladders": "Candidates from precursor ladders",
        "native": "Native or targeted sample",
        "decoy_precursor": "Decoy precursor masses",
        "chimeric_rounds": "Chimeric spectrum search rounds",
        "raw:tol": "Raw spectrum tolerance (ppm)",
        "tag:min_length": "Minimum tag length",
        "tag:max_length": "Maximum tag length",
        "ex:var_mod_file": "Variable modifications file (TopPIC format)"
    },
    "FLASHAnnotator": {
        "algorithm": "Annotation",
        "precursor_charge": "Precursor charge",
        "algorithm:tol": "Fragment tolerance (ppm)",
        "algorithm:calibrate": "Recalibrate m/z",
        "algorithm:calibration_tol": "Calibration tolerance (ppm)",
        "algorithm:min_peaks": "Minimum isotope peaks",
        "algorithm:min_peaks_small": "Minimum isotope peaks of small fragments",
        "algorithm:min_rel_isotope_intensity": "Minimum relative isotope intensity",
        "algorithm:min_cos": "Minimum isotope cosine",
        "algorithm:min_pearson": "Minimum isotope correlation",
        "algorithm:min_mass_per_charge": "Minimum mass per charge",
        "algorithm:max_mass": "Maximum fragment mass (Da)",
        "algorithm:decoy_shifts": "Decoy mass shifts (Da)",
        "algorithm:p1": "Fragment observation probability",
        "algorithm:terminal_calibration": "Terminal fragment score calibration",
        "algorithm:internal_calibration": "Internal fragment score calibration",
        "algorithm:internal_ions": "Annotate internal fragments",
        "algorithm:internal_max_length": "Longest internal fragment (residues)",
        "algorithm:internal_min_tag_length_asp": "Tag length for cleavage after Asp",
        "algorithm:internal_min_tag_length": "Tag length for other cleavages",
        "algorithm:internal_extension": "Internal fragments beyond Asp ladders"
    },
    "FLASHQuantConsensus": {
        "min_run_fraction": "Minimum fraction of runs",
        "mbr_fdr": "Match between runs FDR",
        "id_fdr": "Identification FDR",
        "mbr_min_score": "Minimum match between runs score"
    }
}