Include default cite-seq-count params for CiteSeq handler

Author: bbimber

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -838,7 +838,7 @@ public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcl
 
         if (includeExcludeFailedcDNA)
         {
-            ret.add(ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, true));
+            ret.add(ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, false));
         }
 
         return ret;

singlecell/src/org/labkey/singlecell/analysis/CellHashingHandler.java

@@ -75,7 +75,7 @@ public static List<ToolParameterDescriptor> getDefaultParams(boolean allowScanni
 
         ret.addAll(Arrays.asList(
                 ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 2),
-                ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, true),
+                ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, false),
                 ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5),
                 ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("-cells"), "cells", "Expected Cells", null, "ldk-integerfield", null, 20000),
                 ToolParameterDescriptor.create("tagGroup", "Tag List", null, "ldk-simplelabkeycombo", new JSONObject(){{

singlecell/src/org/labkey/singlecell/analysis/CellRangerSeuratHandler.java

@@ -184,7 +184,7 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 }
             }
 
-            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(),"readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", true), false, false);
+            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(),"readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", false), false, false);
 
             if (ctx.getParams().get(GTF_FILE_ID) == null)
             {

singlecell/src/org/labkey/singlecell/analysis/LoupeCellHashingHandler.java

@@ -89,7 +89,7 @@ public class Processor implements SequenceOutputHandler.SequenceOutputProcessor
         @Override
         public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
         {
-            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", true), true, false);
+            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", false), true, false);
         }
 
         @Override

singlecell/src/org/labkey/singlecell/analysis/SeuratCellHashingHandler.java

@@ -94,7 +94,7 @@ public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Recor
                 }
             }
 
-            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getSourceDirectory(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", true), true, false);
+            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getSourceDirectory(), ctx.getJob(), ctx.getSequenceSupport(), "readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", false), true, false);
         }
 
         @Override

singlecell/src/org/labkey/singlecell/analysis/SeuratCiteSeqHandler.java

@@ -29,7 +29,7 @@ public SeuratCiteSeqHandler()
     {
         super(ModuleLoader.getInstance().getModule(SingleCellModule.class), "Seurat GEX/CITE-seq Counts", "This will run CiteSeqCount to generate a sample-to-cellbarcode TSV based on the cell barcodes present in the saved Seurat object.", null, Arrays.asList(
                 ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 2),
-                ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, true),
+                ToolParameterDescriptor.create("excludeFailedcDNA", "Exclude Failed cDNA", "If selected, cDNAs with non-blank status fields will be omitted", "checkbox", null, false),
                 ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell (Cell Hashing)", null, "ldk-integerfield", null, 5),
                 ToolParameterDescriptor.create("useOutputFileContainer", "Submit to Source File Workbook", "If checked, each job will be submitted to the same workbook as the input file, as opposed to submitting all jobs to the same workbook.  This is primarily useful if submitting a large batch of files to process separately..", "checkbox", new JSONObject()
                 {{
@@ -79,7 +79,7 @@ public class Processor implements SequenceOutputHandler.SequenceOutputProcessor
         @Override
         public void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
         {
-            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(),"readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", true), false, true);
+            CellHashingService.get().prepareHashingAndCiteSeqFilesIfNeeded(ctx.getOutputDir(), ctx.getJob(), ctx.getSequenceSupport(),"readsetId", ctx.getParams().optBoolean("excludeFailedcDNA", false), false, true);
         }
 
         @Override

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

@@ -7,6 +7,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 import org.labkey.api.singlecell.CellHashingService;
 import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellOutput;
@@ -17,7 +18,7 @@
 import org.labkey.singlecell.analysis.SeuratCiteSeqHandler;
 
 import java.io.File;
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -35,16 +36,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("AppendCiteSeq", "Possibly Append CITE-seq Data", "OOSAP", "If available, this will process and append CITE-seq data to the Seurat object(s).", Arrays.asList(
-                SeuratToolParameter.create("normalizationMethod", "Normalization Method", "", "ldk-simplecombo", new JSONObject(){{
-                    put("storeValues", "CLR");
-                    put("initialValues", "CLR");
-                }}, "CLR"),
-                SeuratToolParameter.create("processingMethod", "Processing Method", "", "ldk-simplecombo", new JSONObject(){{
-                    put("storeValues", "PCA-tSNE;Distance-tSNE");
-                    put("initialValues", "PCA-tSNE");
-                }}, "PCA-tSNE")
-            ), null, null);
+            super("AppendCiteSeq", "Possibly Append CITE-seq Data", "OOSAP", "If available, this will process and append CITE-seq data to the Seurat object(s).", getParams(), null, null);
         }
 
         @Override
@@ -54,6 +46,23 @@ public AppendCiteSeq create(PipelineContext ctx)
         }
     }
 
+    private static List<ToolParameterDescriptor> getParams()
+    {
+        List<ToolParameterDescriptor> ret = new ArrayList<>();
+        ret.add(SeuratToolParameter.create("normalizationMethod", "Normalization Method", "", "ldk-simplecombo", new JSONObject(){{
+            put("storeValues", "CLR");
+            put("initialValues", "CLR");
+        }}, "CLR"));
+        ret.add(SeuratToolParameter.create("processingMethod", "Processing Method", "", "ldk-simplecombo", new JSONObject(){{
+            put("storeValues", "PCA-tSNE;Distance-tSNE");
+            put("initialValues", "PCA-tSNE");
+        }}, "PCA-tSNE"));
+
+        ret.addAll(CellHashingService.get().getDefaultHashingParams(false));
+
+        return ret;
+    }
+
     @Override
     public Collection<String> getRLibraries()
     {