Update scGate to use consensusModels argument

Author: bbimber

singlecell/resources/chunks/RunScGate.R

@@ -1,7 +1,7 @@
 for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues)
+    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels)
 
     saveData(seuratObj, datasetId)
 }

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

@@ -21,6 +21,15 @@ public Provider()
         {
             super("RunScGate", "Run scGate", "scGate", "This will run scGate with the default built-in models and create a consensus call.", Arrays.asList(
                     SeuratToolParameter.create("modelNames", "Model(s)", "The set of scGate modules to test.", "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", true);
+                        put("allowBlank", false);
+                        put("storeValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
+                        put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Epithelial;Epithelial;Platelet_MK");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, null, null, true, true),
+                    SeuratToolParameter.create("consensusModels", "Models for Consensus", "The subset of models to be considered for the consensus call.", "ldk-simplecombo", new JSONObject()
                     {{
                         put("multiSelect", true);
                         put("allowBlank", false);