diff --git a/jsons/parameters.json b/jsons/parameters.json index 382c97c..2b862f4 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -3371,8 +3371,10 @@ "pglyco_db_style_1": "process", "pipi_style_1": "thread_num", "pnovo_style_1": "thread", + "precursor_window_scanner_style_1": "--cpus", "proteomics_qc_style_1": "n_cpus", "ptmshepherd_style_1": "threads", + "reporter_extract_style_1": "--cpus", "ucontroller_style_1": "cpus", "ursgal_style_1": "cpus", "xtandem_style_1": "spectrum, threads" @@ -3467,6 +3469,18 @@ "max - 1" ] ], + "precursor_window_scanner_style_1": [ + [ + -1, + -1 + ] + ], + "reporter_extract_style_1": [ + [ + -1, + -1 + ] + ], "ucontroller_style_1": [ [ -1, @@ -10980,6 +10994,7 @@ "mzml2mgf_style_1": "ms_level", "pipi_style_1": "ms_level", "pyqms_style_1": "ms_level", + "reporter_extract_style_1": "--ms_level", "sugarpy_plot_style_1": "ms_level", "sugarpy_run_style_1": "ms_level", "ursgal_style_1": "ms_level" @@ -14118,6 +14133,22 @@ "value_translations": {}, "value_type": "bool" }, + { + "default_value": "TMTpro", + "description": "Reporter Ion type", + "key_translations": { + "reporter_extract_style_1": "--quant_method", + "ursgal_style_1": "reporter_ion_type" + }, + "name": "reporter_ion_type", + "tag": [ + "quantification", + "MSn" + ], + "triggers_rerun": true, + "value_translations": {}, + "value_type": "str" + }, { "default_value": false, "description": "Require MS/MS match in condition to consider quantification", diff --git a/jsons/styles.json b/jsons/styles.json index ee09c1c..6fdf0e4 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -271,6 +271,14 @@ "1.0.0" ] }, + { + "name": "Precursor Window Scanner Style 1", + "reference": "Mathieson T. and Sweetman, G. (2021)", + "style": "precursor_window_scanner_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "Proteomics Quality Control", "reference": "Ursgal2 Team", @@ -295,6 +303,14 @@ "1.0.0" ] }, + { + "name": "Reporter Extract Style 1", + "reference": "Mathieson T., Sweetman, G. and Fufezan, C. (2021)", + "style": "reporter_extract_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "Sanitize CSV", "reference": "Ursgal2 Team", @@ -572,17 +588,17 @@ ] }, { - "name": "mx_qc_style_1", + "name": "mx_gsk_style_1", "reference": "Ursgal2 Team", - "style": "mx_qc_style_1", + "style": "mx_gsk_style_1", "versions": [ "1.0.0" ] }, { - "name": "mx_gsk_style_1", + "name": "mx_qc_style_1", "reference": "Ursgal2 Team", - "style": "mx_gsk_style_1", + "style": "mx_qc_style_1", "versions": [ "1.0.0" ] @@ -687,6 +703,14 @@ "1.0.0" ] }, + { + "name": "spectrum_meta_data_style_1", + "reference": "Ursgal2 Team", + "style": "spectrum_meta_data_style_1", + "versions": [ + "1.0.0" + ] + }, { "name": "test_node_style_1", "reference": "Ursgal2 Team", @@ -718,13 +742,5 @@ "versions": [ "1.0.0" ] - }, - { - "name": "spectrum_meta_data_style_1", - "reference": "Ursgal2 Team", - "style": "spectrum_meta_data_style_1", - "versions": [ - "1.0.0" - ] } ] \ No newline at end of file