Merge pull request #91 from uparma/mx/calculate_ion_charge_state

* added params for calculate_ion_charge_state_style_1
uparma · Jun 17, 2022 · 10f4bed · 10f4bed
2 parents 5619497 + de57739
commit 10f4bed
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Showing 2 changed files with 49 additions and 0 deletions.
diff --git 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
@@ -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"
   }
 ]