Strip quotes from many scRNA-seq fields

Author: bbimber

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

@@ -27,6 +27,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, "cDNA_ID").delimiter(","),
                     SeuratToolParameter.create("addMetadata", "Query Metadata?", "If checked, Rdiscvr::QueryAndApplyMetadataUsingCDNA will be run after aggregation. This requires a cDNA_ID column to exist.", "checkbox", new JSONObject(){{
                         put("checked", true);

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

@@ -26,10 +26,12 @@ public Provider()
                     SeuratToolParameter.create("adtWhitelist", "ADT Whitelist", "If provided, these ADTs will be scaled and used for PCA. If empty, all ADTs will be used.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("adtBlacklist", "ADT Blacklist", "If provided, these ADTs will be excluded from scaling/PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("assayName", "Assay Name", "The assay to use", "textbox", new JSONObject(){{
 

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

@@ -41,10 +41,12 @@ public Provider()
                     SeuratToolParameter.create("featureWhitelist", "Genes to Add to VariableFeatures", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("featureExclusionList", "Genes to Exclude From VariableFeatures", "These genes, entered comma-separated or one/line, will be excluded from the genes passed to RunPCA (which is otherwise determined by Seurat::VariableFeatures)", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(",")
                     ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }

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

@@ -29,6 +29,7 @@ public Provider()
                         put("height", 150);
                         put("width", 600);
                         put("delimiter", DELIM);
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null),
                     SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
 

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

@@ -26,6 +26,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(",")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }

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

@@ -26,6 +26,7 @@ public Provider()
                     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 unique value of BarcodePrefix. If blank, each object will be treated as one unit of data.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null, "subsetFields", true, true).delimiter(","),
                     SeuratToolParameter.create("seed", "Random Seed", "This random seed, used for downsampling", "ldk-integerfield", new JSONObject(){{
 

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

@@ -21,11 +21,12 @@ public Provider()
         {
             super("DropAssays", "Assay(s) to Drop", "Seurat", "This will drop the selected assays from your Seurat object(s)", Arrays.asList(
                 SeuratToolParameter.create("assayNames", "Assay(s)", "The names of assays to drop, such as: RNA.orig, ADT, or RNA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
-                            put("allowBlank", false);
-                            put("height", 150);
-                            put("delimiter", ",");
-                        }}, null).delimiter(",")
-                ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+                    put("allowBlank", false);
+                    put("height", 150);
+                    put("delimiter", ",");
+                    put("stripCharsRe", "/['\"]/g");
+                }}, null).delimiter(",")
+            ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 
         @Override

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

@@ -26,6 +26,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(",")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }

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

@@ -28,6 +28,7 @@ public Provider()
                         put("allowBlank", false);
                         put("height", 200);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("testsToUse", "Tests To Use", "The set of tests to perform.", "ldk-simplecombo", new JSONObject()
                     {{

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

@@ -36,10 +36,12 @@ public Provider()
                     SeuratToolParameter.create("integrationFeaturesInclusionList", "Genes to Add to Integration", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("integrationFeaturesExclusionList", "Genes to Exclude From Integration", "These genes, entered comma-separated or one/line, will be excluded from the genes passed to RunPCA (which is otherwise determined by Seurat::VariableFeatures)", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
                     }}, null).delimiter(","),
                     SeuratToolParameter.create("kWeight", "k.weight", "This will be passed to k.weight on Seurat::IntegrateData", "ldk-integerfield", new JSONObject(){{
                         put("allowBlank", false);