Merge pull request #96 from uparma/mx/select_ions

* select_ions params
uparma · Jul 28, 2022 · 4742d1d · 4742d1d
2 parents 17ef733 + 7ca3860
commit 4742d1d
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diff --git a/jsons/parameters.json b/jsons/parameters.json
@@ -3048,6 +3048,7 @@
         "description": "threshold value for correlation analysis to be considered acceptable.",
         "key_translations": {
             "calculate_ion_charge_state_style_1": "min_corr",
+            "select_ions_style_1": "tic_thr",
             "ursgal_style_1": "correlation_threshold"
         },
         "name": "correlation_threshold",
@@ -8526,6 +8527,32 @@
         "value_translations": {},
         "value_type": "list"
     },
+    {
+        "default_value": true,
+        "description": "flag whether to keep non-annotated ions.",
+        "key_translations": {
+            "select_ions_style_1": "keep_non_annotated_metabolites",
+            "ursgal_style_1": "keep_non_annotated_metabolites"
+        },
+        "name": "keep_non_annotated_metabolites",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "bool"
+    },
+    {
+        "default_value": true,
+        "description": "flag whether to keep ions without detected charge.",
+        "key_translations": {
+            "select_ions_style_1": "keep_uncharged_ions",
+            "ursgal_style_1": "keep_uncharged_ions"
+        },
+        "name": "keep_uncharged_ions",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "bool"
+    },
     {
         "default_value": "rbf",
         "description": "The kernel function of the support vector machine used for PSM post-processing ('rbf', 'linear', 'poly' or 'sigmoid')",
@@ -9976,6 +10003,19 @@
         "value_translations": {},
         "value_type": "int"
     },
+    {
+        "default_value": 0.0,
+        "description": "Minimum percentage of samples in which ion needs to be detected for keeping (0 = keep all ions, 100 = keep only ions detected in all samples).",
+        "key_translations": {
+            "select_ions_style_1": "det_thr",
+            "ursgal_style_1": "min_percentage_detected_ions_samples"
+        },
+        "name": "min_percentage_detected_ions",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "float"
+    },
     {
         "default_value": 1,
         "description": "Minimum number of precursors that match a spectrum.",
@@ -14056,6 +14096,19 @@
         "value_translations": {},
         "value_type": "int"
     },
+    {
+        "default_value": 0.0,
+        "description": "Average fraction of scans above which ion should be detected in order to include (not too stringent to allow for further filtering below).",
+        "key_translations": {
+            "select_ions_style_1": "scan_thr",
+            "ursgal_style_1": "scan_fraction_threshold"
+        },
+        "name": "scan_threshold",
+        "tag": [],
+        "triggers_rerun": true,
+        "value_translations": {},
+        "value_type": "float"
+    },
     {
         "default_value": true,
         "description": "Use correlation correction to score?",

diff --git a/jsons/styles.json b/jsons/styles.json
@@ -646,5 +646,13 @@
       "1.0.0"
     ],
     "reference": "Ursgal2 Team"
+  },
+  {
+    "style": "select_ions_style_1",
+    "name": "select_ions_style_1",
+    "versions": [
+      "1.0.0"
+    ],
+    "reference": "Ursgal2 Team"
   }
 ]