diff --git a/jsons/parameters.json b/jsons/parameters.json index f033b11..9c18034 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3011,6 +3011,19 @@ "value_translations": {}, "value_type": "bool" }, + { + "default_value": 0.75, + "description": "threshold value for correlation analysis to be considered acceptable.", + "key_translations": { + "calculate_ion_charge_state_style_1": "min_corr", + "ursgal_style_1": "correlation_threshold" + }, + "name": "correlation_threshold", + "tag": [], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "float" + }, { "default_value": true, "description": "the number of unique hits for each identifier is given in separate columns for each raw file (file name as defiened in Spectrum Title)", @@ -8304,6 +8317,7 @@ "default_value": "positive", "description": "The ion mode that has been used for acquiring mass spectra (positive or negative)", "key_translations": { + "calculate_ion_charge_state_style_1": "polarity", "mx_gsk_stage2_qc_style_1": "polarity", "mzml2mgf_style_1": "ion_mode", "recalibrate_mz_global_style_1": "polarity", @@ -8390,6 +8404,19 @@ "value_translations": {}, "value_type": "float" }, + { + "default_value": 0.0025, + "description": "m/z tolerance of detecting isotopologue peaks for charge calculation", + "key_translations": { + "calculate_ion_charge_state_style_1": "tol_iso", + "ursgal_style_1": "isotopologue_mass_tolerance" + }, + "name": "isotopologue_mass_tolerance", + "tag": [], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "float" + }, { "default_value": ".u.json", "description": "Exension for .json files", @@ -9682,6 +9709,19 @@ "value_translations": {}, "value_type": "list" }, + { + "default_value": 2, + "description": "minimum number of adjacent peaks e.g for charge calculation", + "key_translations": { + "calculate_ion_charge_state_style_1": "min_zmers", + "ursgal_style_1": "min_adj_peaks" + }, + "name": "min_adj_peaks", + "tag": [], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "int" + }, { "default_value": 0.1, "description": "minimum distance to neighbour", @@ -12767,6 +12807,7 @@ "default_value": 5, "description": "Maximal accepted parent ion charge", "key_translations": { + "calculate_ion_charge_state_style_1": "max_charge", "comet_style_1": "max_precursor_charge", "mascot_style_1": "CHARGE_max", "msamanda_style_1": "considered_charges_max", diff --git a/jsons/styles.json b/jsons/styles.json index 502d382..561f3fc 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -622,5 +622,13 @@ "1.0.0" ], "reference": "Ursgal2 Team" + }, + { + "style": "calculate_ion_charge_state_style_1", + "name": "calculate_ion_charge_state_style_1", + "versions": [ + "1.0.0" + ], + "reference": "Ursgal2 Team" } ]