Update SDA args

Author: bbimber

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunSDA.java

@@ -43,10 +43,16 @@ public Provider()
                         put("delimiter", ",");
                         put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
                     }}, null).delimiter(","),
-                    SeuratToolParameter.create("minAsinhThreshold", "asinh Threshold", "This is used to filter genes. Only features with asinh(TOTAL_COUNTS) above this value are included.", "ldk-numberfield", new JSONObject(){{
+                    SeuratToolParameter.create("minFeatureCount", "Min Feature Count", "This is used to filter genes. Only features with total expression across all cells above this value are included. The default of 5 is designed to include effectively all but the most lowly expressed genes", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 5, "minFeatureCount", false),
+                    SeuratToolParameter.create("minCellsExpressingFeature", "Min Cells Expressing Feature", "Can be used with perCellExpressionThreshold to drop features present in limited cells. Only features detected above perCellExpressionThreshold in at least minCellsExpressingFeature will be retained. If this value is less than zero it is interpreted as a percentage of total cells. If above zero it is interpeted as the min number of cells", "ldk-numberfield", new JSONObject(){{
                         put("minValue", 0);
                         put("decimalPrecision", 2);
-                    }}, 0.5, "minAsinhThreshold", false),
+                    }}, 0.5, "minCellsExpressingFeature", false),
+                    SeuratToolParameter.create("perCellExpressionThreshold", "Per Cell Expression Threshold", "Can be used with perCellExpressionThreshold to drop features present in limited cells. Only features detected above perCellExpressionThreshold in at least minCellsExpressingFeature will be retained", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 0, "perCellExpressionThreshold", false),
                     SeuratToolParameter.create("minLibrarySize", "Min Library Size", "Passed to dropsim::normaliseDGE() min_library_size", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, 50),