Expose ability to keep ambiguous features with AppendNimble

Author: bbimber

singlecell/resources/chunks/AppendNimble.R

@@ -11,8 +11,7 @@ for (datasetId in names(seuratObjects)) {
   seuratObj <- readRDS(seuratObjects[[datasetId]])
 
   for (genomeId in names(nimbleGenomes)) {
-    #TODO: dropAmbiguousFeatures
-    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE)
+    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, dropAmbiguousFeatures = !retainAmbiguousFeatures)
   }
 
   saveData(seuratObj, datasetId)

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

@@ -30,7 +30,11 @@ public Provider()
                     ToolParameterDescriptor.create("nimbleGenomes", "Genomes", "Genomes to include", "singlecell-nimbleappendpanel", new JSONObject()
                     {{
                         put("allowBlank", false);
-                    }}, null)
+                    }}, null),
+                    ToolParameterDescriptor.create("retainAmbiguousFeatures", "Retain Ambiguous Features", "If checked, features hitting more than one reference will be retained", "checkbox", new JSONObject()
+                    {{
+                        put("check", false);
+                    }}, false)
             ), Arrays.asList("sequenceanalysis/field/GenomeField.js", "/singlecell/panel/NimbleAppendPanel.js"), null);
         }