Merge pull request #107 from uparma/feature/extract_reporter

Feature/extract reporter
uparma · Sep 29, 2022 · d4188d9 · d4188d9
2 parents fcf863b + 18bc6bc
commit d4188d9
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Showing 2 changed files with 59 additions and 12 deletions.
diff --git 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
@@ -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"
-        ]
     }
 ]