Allow user to set minEDS

Author: bbimber

singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R

@@ -16,8 +16,8 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)
   }
 
-  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRA', storeStimLevelData = FALSE)
-  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRB')
+  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRA', storeStimLevelData = FALSE, minEDS = minEDS)
+  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRB', minEDS = minEDS)
 
   saveData(seuratObj, datasetId)
 

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

@@ -2,6 +2,7 @@
 
 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;
@@ -17,7 +18,9 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("IdentifyAndStoreActiveClonotypes", "Identify And Store Active Clonotypes", "Rdiscvr", "This uses RDiscvr::IdentifyAndStoreActiveClonotypes to predict TCR-triggered T cells and save the results to the database", List.of(), null, null);
+            super("IdentifyAndStoreActiveClonotypes", "Identify And Store Active Clonotypes", "Rdiscvr", "This uses RDiscvr::IdentifyAndStoreActiveClonotypes to predict TCR-triggered T cells and save the results to the database", List.of(
+                SeuratToolParameter.create("minEDS", "Min EDS", "If provided, only cells with an EffectorDifferentiationScore (EDS) above this value will be included", "ldk-integerfield", null, 2.0, null, true)
+            ), null, null);
         }