Support inclusion/exclusion lists for ApplyKnownClonotypicData

Author: bbimber

singlecell/resources/chunks/ApplyKnownClonotypicData.R

@@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- ApplyKnownClonotypicData(seuratObj)
+    seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList)
     saveData(seuratObj, datasetId)
 
     # Cleanup

singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.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.List;
@@ -18,8 +20,21 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("ApplyKnownClonotypicData", "Append Known Clonotype/Antigen Data", "RDiscvr", "This will query the clone_responses table and append a column tagging each cell for matching antigens (based on clonotype)", List.of(
-
-            ), null, null);
+                    SeuratToolParameter.create("antigenInclusionList", "Antigen(s) to Include", "Enter antigens, per line. Only stims using these antigens will be used", "sequenceanalysis-trimmingtextarea", new JSONObject()
+                    {{
+                        put("allowBlank", false);
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
+                    }}, null, null, true, true).delimiter(","),
+                    SeuratToolParameter.create("antigenExclusionList", "Antigen(s) to Exclude", "Enter antigens, per line. Stims using these antigens will be excluded", "sequenceanalysis-trimmingtextarea", new JSONObject()
+                    {{
+                        put("allowBlank", false);
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
+                    }}, null, null, true, true).delimiter(",")
+            ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }