Support custom gates when running scGate

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 = c('Bcell', 'Tcell', 'NK', 'Myeloid'), labelRename = list(Tcell = 'T_NK', NK = 'T_NK'))
+    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'))
 
     saveData(seuratObj, datasetId)
 }

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

@@ -1,7 +1,9 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.json.JSONObject;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
@@ -18,7 +20,15 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         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");
+                        put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, null, null, true, true)
             ), null, null);
         }