Merge pull request #90 from uparma/mx/recalibrate_mz_global_params

added style and params for global mz recal node
uparma · Jun 13, 2022 · 5619497 · 5619497
2 parents babc7ca + 1a09c6d
commit 5619497
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diff --git a/jsons/parameters.json b/jsons/parameters.json
@@ -84,6 +84,19 @@
         "value_translations": {},
         "value_type": "dict"
     },
+    {
+        "default_value": 0.005,
+        "description": "absolute mass tolerance for post-acquisition mass axis re-calibration",
+        "key_translations": {
+            "recalibrate_mz_global_style_1": "delta_abs_t",
+            "ursgal_style_1": "absolute_mass_tolerance"
+        },
+        "name": "absolute_mass_tolerance",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "float"
+    },
     {
         "default_value": false,
         "description": "If True, multiple PSMs for one spectrum can be reported if their score difference is below the threshold. If False, all PSMs for one spectrum are removed if the score difference between the best and secondbest PSM is not above the threshold, i.e. if there are conflicting PSMs with similar scores.",
@@ -135,6 +148,21 @@
         },
         "value_type": "bool"
     },
+    {
+        "default_value": [
+            "A"
+        ],
+        "description": "empirical adduct confidence; A = stringent, B = acceptable, C = tentative, D = speculative. List of all levels to be considered for mass calibration.",
+        "key_translations": {
+            "recalibrate_mz_global_style_1": "confidence_level",
+            "ursgal_style_1": "adduct_confidence"
+        },
+        "name": "adduct_confidence",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "list"
+    },
     {
         "default_value": false,
         "description": " Static mods are not considered ",
@@ -3542,6 +3570,19 @@
         "value_translations": {},
         "value_type": "bool"
     },
+    {
+        "default_value": 2,
+        "description": "Degrees of freedom for polynomial fit.",
+        "key_translations": {
+            "recalibrate_mz_global_style_1": "poly_degree",
+            "ursgal_style_1": "degrees_of_freedom"
+        },
+        "name": "degrees_of_freedom",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "int"
+    },
     {
         "default_value": "perform_deisotoping",
         "description": "Perform Deisotoping for MS2 spectra. Options are: \"none\", \"deisotope_with_singleton_charge_one\", \"perform_deisotoping\"",
@@ -8265,6 +8306,7 @@
         "key_translations": {
             "mx_gsk_stage2_qc_style_1": "polarity",
             "mzml2mgf_style_1": "ion_mode",
+            "recalibrate_mz_global_style_1": "polarity",
             "recalibrate_mz_style_1": "polarity",
             "ursgal_style_1": "ion_mode"
         },
@@ -9947,6 +9989,7 @@
         "description": "A floating point number indicating the minimum intensity value for the input peaks.",
         "key_translations": {
             "comet_style_1": "minimum_intensity",
+            "recalibrate_mz_global_style_1": "min_int",
             "ursgal_style_1": "minimum_intensity"
         },
         "name": "minimum_intensity",
@@ -12177,6 +12220,19 @@
         "value_translations": {},
         "value_type": "dict"
     },
+    {
+        "default_value": 10,
+        "description": "PPM mass tolerance for post-acquisition mass axis re-calibration",
+        "key_translations": {
+            "recalibrate_mz_global_style_1": "delta_ppm_t",
+            "ursgal_style_1": "ppm_mass_tolerance"
+        },
+        "name": "ppm_mass_tolerance",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "int"
+    },
     {
         "default_value": "linear",
         "description": "charge dependency of precursor mass tolerance (none or linear)",

diff --git a/jsons/styles.json b/jsons/styles.json
@@ -614,5 +614,13 @@
       "1.0.0"
     ],
     "reference": "Ursgal2 Team"
+  },
+  {
+    "style": "recalibrate_mz_global_style_1",
+    "name": "recalibrate_mz_global_style_1",
+    "versions": [
+      "1.0.0"
+    ],
+    "reference": "Ursgal2 Team"
   }
 ]