Expand tcrClust3 wrapper

Author: bbimber

singlecell/resources/chunks/PerformTcrClustering.R

@@ -4,7 +4,8 @@ for (datasetId in names(seuratObjects)) {
 
     seuratObj <- tcrClustR::CalculateTcrDistances(
       inputData = seuratObj,
-      chains = c('TRA', 'TRB'),
+      chains = c('TRA', 'TRB', 'TRG', 'TRD'),
+      organism = organism,
       minimumCloneSize = 2,
       calculateChainPairs = TRUE
     )

singlecell/src/org/labkey/singlecell/pipeline/singlecell/PerformTcrClustering.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;
@@ -18,7 +20,15 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("tcrClustR", "tcrClustR", "tcrClustR", "This will run tcrClustR to cluster TCRs by similarity.", List.of(
-
+                SeuratToolParameter.create("organism", "Organism", "The organism to use",  "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", true);
+                        put("allowBlank", false);
+                        put("storeValues", "human;rhesus;mouse");
+                        put("initialValues", "human");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, null)
             ), null, "https://github.com/bimberlabinternal/tcrClustR/");
         }