Minor improvements to seurat steps

Author: bbimber

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

@@ -24,7 +24,7 @@ public Provider()
                         put("allowBlank", false);
                     }}, null),
                     SeuratToolParameter.create("subsetFields", "Additional Grouping Fields", "A comma-separated list of fields that will be used to subset data within each seurat object. For example, if 'barcodePrefix' is provided and 500 target cells is selected, each incoming seurat object will be subset to no more than 500 cells per barcodePrefix. If blank, each object will be treated as one unit of data.", "textfield", new JSONObject(){{
-                        put("allowBlank", false);
+
                     }}, null),
                     SeuratToolParameter.create("seed", "Random Seed", "This random seed, used for downsampling", "ldk-integerfield", new JSONObject(){{
 

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

@@ -33,6 +33,10 @@ public Provider()
                         put("height", 150);
                         put("delimiter", ",");
                     }}, null),
+                    SeuratToolParameter.create("featuresToRegress", "Features to Regress", "These features, entered comma-separated or one/line, will be passed to Seurat::ScaleData vars.to.regress", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, "nCount_RNA,p.mito"),
                     SeuratToolParameter.create("scaleVariableFeaturesOnly", "ScaleData On Variable Features Only", "If checked, ScaleData will only be performed on VariableFeatures, which should dramatically reduce time and memory", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true),