Support additional seurat options

Author: bbimber

singlecell/resources/chunks/CiteSeqDimRedux.R

@@ -3,7 +3,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObjects[[datasetId]] <- NULL
 
     #TODO: what if not used?
-    seuratObj <- CellMembrane::CiteSeqDimRedux(seuratObj)
+    seuratObj <- bindArgs(CellMembrane::CiteSeqDimRedux, seuratObj)()
 
     newSeuratObjects[[datasetId]] <- seuratObj
 

singlecell/resources/chunks/FindMarkers.R

@@ -3,7 +3,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObjects[[datasetId]] <- NULL
 
     outFile = paste0(datasetId, '.markers.txt')
-    dt <- bindArgs(CellMembrane::Find_Markers, seuratObj)
+    dt <- bindArgs(CellMembrane::Find_Markers, seuratObj)()
     print(dt)
 
     # Cleanup

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqDimRedux.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.Arrays;
@@ -18,7 +20,9 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("CiteSeqDimRedux", "CiteSeq DimRedux", "CellMembrane/Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
-
+                    SeuratToolParameter.create("performClrNormalization", "Perform CLR Normalization", "If true, Seurat CLR normalization will be performed. Otherwise any pre-existing normalization is used.", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true, "performClrNormalization", true)
             ), null, null);
         }