Allow jobs to control more EmptyDrop options

Author: bbimber

singlecell/resources/chunks/PrepareRawCounts.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     rawCountDir <- seuratObjects[[datasetId]]
 
     datasetName <- datasetIdToName[[datasetId]]
-    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName)
+    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold)
 
     saveData(seuratObj, datasetId)
 

singlecell/resources/web/singlecell/panel/SingleCellProcessingPanel.js

@@ -6,6 +6,8 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
     jobType: 'singleCell',
 
     initComponent: function(){
+        this.showPrepareRawData = this.handlerClass === 'ProcessSingleCellHandler';
+
         Ext4.apply(this, {
             itemId: 'sequenceAnalysisPanel',
             buttonAlign: 'left',
@@ -198,6 +200,28 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
     },
 
     onDataLoad: function(results){
+        results.prepareRawData = [{
+            description: 'Options related to processing the 10x matrix into a seurat object',
+            label: 'Prepare Raw Counts',
+            name: 'PrepareRawCounts',
+            parameters: [{
+                fieldXtype: 'ldk-integerfield',
+                    name: 'emptyDropsLower',
+                label: 'EmptyDrops Lower',
+                description: 'Passed to DropletUtils::emptyDrops lower argument',
+                defaultValue: 200,
+                minValue: 0
+            },{
+                fieldXtype: 'ldk-numberfield',
+                name: 'emptyDropsFdrThreshold',
+                label: 'EmptyDrops FDR Threshold',
+                description: 'The FDR limit used to filter the results of DropletUtils::emptyDrops',
+                defaultValue: 0.001,
+                minValue: 0,
+                decimalPrecision: 4
+            }]
+        }];
+
         this.add([this.getFilePanelCfg(), this.getProtocolPanelCfg(),{
             xtype: 'panel',
             title: 'Analysis Options',
@@ -212,6 +236,17 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
         var panel = this.down('#analysisOptions');
 
         var items = [];
+        if (this.showPrepareRawData){
+            items.push({
+                xtype: 'sequenceanalysis-analysissectionpanel',
+                title: 'Prepare Raw Data',
+                stepType: 'prepareRawData',
+                singleTool: true,
+                sectionDescription: 'This section allows you to control the parsing of the raw 10x count data',
+                toolConfig: results
+            });
+        }
+
         items.push({
             xtype: 'sequenceanalysis-analysissectionpanel',
             title: 'Seurat Processing',

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

@@ -1,10 +1,14 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.labkey.api.pipeline.PipelineJobException;
 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.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
+import java.util.List;
 
 public class PrepareRawCounts extends AbstractCellMembraneStep
 {
@@ -20,11 +24,11 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("PrepareRawCounts", LABEL, "CellMembrane/Seurat", "This step reads the raw count matrix/matrices, and runs EmptyDrops to provide an unfiltered count matrix.", Arrays.asList(
-
+                    SeuratToolParameter.create("emptyDropsLower", "Lower", "Passed to DropletUtils::emptyDrops lower argument", "ldk-integerfield", null, 200),
+                    SeuratToolParameter.create("emptyDropsFdrThreshold", "FDR Threshold", "The FDR limit used to filter the results of DropletUtils::emptyDrops", "ldk-numberfield", null, 0.001)
             ), null, null);
         }
 
-
         @Override
         public PrepareRawCounts create(PipelineContext ctx)
         {