Allow tcrClustR to specify a subset of chains

Author: bbimber

singlecell/resources/chunks/PerformTcrClustering.R

@@ -5,7 +5,7 @@ for (datasetId in names(seuratObjects)) {
     print(paste0('Calculating distances for: ', datasetId))
     seuratObj <- tcrClustR::CalculateTcrDistances(
       inputData = seuratObj,
-      chains = c('TRA', 'TRB', 'TRG', 'TRD'),
+      chains = chains,
       organism = organism,
       minimumCloneSize = 2,
       calculateChainPairs = TRUE

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

@@ -28,7 +28,16 @@ public Provider()
                         put("initialValues", "human");
                         put("delimiter", ";");
                         put("joinReturnValue", true);
-                    }}, null)
+                    }}, null),
+                    SeuratToolParameter.create("chains", "Chains", "The chains to process",  "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", true);
+                        put("allowBlank", false);
+                        put("storeValues", "TRA;TRB;TRG;TRD");
+                        put("initialValues", "TRA;TRB;TRG;TRD");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, "TRA;TRB;TRG;TRD", null, true, true)
             ), null, "https://github.com/bimberlabinternal/tcrClustR/");
         }