Update DefaultNimbleAppend params

Author: bbimber

singlecell/resources/chunks/PerformDefaultNimbleAppend.R

@@ -16,7 +16,7 @@ for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-  seuratObj <- Rdiscvr::PerformDefaultNimbleAppend(seuratObj)
+  seuratObj <- Rdiscvr::PerformDefaultNimbleAppend(seuratObj, appendMHC = appendMHC, appendKIR = appendKIR, appendNKG = appendNKG, appendIG = appendIG, appendViral = appendViral)
 
   saveData(seuratObj, datasetId)
 

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

@@ -1,9 +1,13 @@
 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;
+
 public class PerformDefaultNimbleAppend extends AbstractRDiscvrStep
 {
     public PerformDefaultNimbleAppend(PipelineContext ctx, PerformDefaultNimbleAppend.Provider provider)
@@ -15,7 +19,23 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("PerformDefaultNimbleAppend", "Default Nimble Append", "RDiscvr", "This uses Rdiscvr to run the default nimble append, adding MHC, KIR, NKG, Viral and Ig data", null, null, null);
+            super("PerformDefaultNimbleAppend", "Default Nimble Append", "RDiscvr", "This uses Rdiscvr to run the default nimble append, adding MHC, KIR, NKG, Viral and Ig data", Arrays.asList(
+                    SeuratToolParameter.create("appendMHC", "Append MHC", "If true, MHC data will be appended", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("appendKIR", "Append KIR", "If true, KIR data will be appended", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("appendNKG", "Append NKG2", "If true, NKG2 data will be appended", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("appendIG", "Append Ig", "If true, immunoglobulin data will be appended", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("appendViral", "Append Viral", "If true, viral data will be appended", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true)
+            ), null, null);
         }
 
         @Override