Allow R params to be skipped

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -337,7 +337,11 @@ protected Chunk createParamChunk(List<SeuratObjectWrapper> inputObjects, String
         {
             if (pd instanceof SeuratToolParameter)
             {
-                body.add(((SeuratToolParameter) pd).getVariableName() + " <- " + prepareValueForR((SeuratToolParameter)pd));
+                SeuratToolParameter stp = (SeuratToolParameter)pd;
+                if (stp.shouldIncludeInMarkdown(getPipelineCtx().getJob(), getProvider(), getStepIdx()))
+                {
+                    body.add(((SeuratToolParameter) pd).getVariableName() + " <- " + prepareValueForR(stp));
+                }
             }
         }
         body.add("");

singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java

@@ -1,32 +1,47 @@
 package org.labkey.api.singlecell.pipeline;
 
+import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.Nullable;
 import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
 
 public class SeuratToolParameter extends ToolParameterDescriptor
 {
     private String _rName;
+    private boolean _includeIfEmptyOrNull;
 
-    public SeuratToolParameter(String name, String label, String description, String fieldXtype, @Nullable Object defaultValue, @Nullable JSONObject additionalExtConfig, String rName)
+    public SeuratToolParameter(String name, String label, String description, String fieldXtype, @Nullable Object defaultValue, @Nullable JSONObject additionalExtConfig, String rName, boolean includeIfEmptyOrNull)
     {
         super(null, name, label, description, fieldXtype, defaultValue, additionalExtConfig);
 
         _rName = rName;
+        _includeIfEmptyOrNull = includeIfEmptyOrNull;
     }
 
     public static SeuratToolParameter create(String name, String label, String description, String fieldXtype, @Nullable JSONObject additionalExtConfig, @Nullable Object defaultValue)
     {
-        return new SeuratToolParameter(name, label, description, fieldXtype, defaultValue, additionalExtConfig, null);
+        return new SeuratToolParameter(name, label, description, fieldXtype, defaultValue, additionalExtConfig, null, true);
     }
 
-    public static SeuratToolParameter create(String name, String label, String description, String fieldXtype, @Nullable JSONObject additionalExtConfig, @Nullable Object defaultValue, String rName)
+    public static SeuratToolParameter create(String name, String label, String description, String fieldXtype, @Nullable JSONObject additionalExtConfig, @Nullable Object defaultValue, String rName, boolean includeIfEmptyOrNull)
     {
-        return new SeuratToolParameter(name, label, description, fieldXtype, defaultValue, additionalExtConfig, rName);
+        return new SeuratToolParameter(name, label, description, fieldXtype, defaultValue, additionalExtConfig, rName, includeIfEmptyOrNull);
     }
 
     public String getVariableName()
     {
         return _rName == null ? getName() : _rName;
     }
+
+    public boolean shouldIncludeInMarkdown(PipelineJob job, PipelineStepProvider provider, int stepIdx)
+    {
+        if (!_includeIfEmptyOrNull)
+        {
+            return StringUtils.trimToNull(extractValue(job, provider, stepIdx)) != null;
+        }
+
+        return true;
+    }
 }

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

@@ -22,24 +22,24 @@ public Provider()
             super("FilterRawCounts", "Filter Raw Counts", "Seurat/OOSAP", "This will use OOSAP/Seurat to perform basic filtering on cells based on UMI count, feature count, etc.", Arrays.asList(
                     SeuratToolParameter.create("nCountRnaLow", "Min UMI Count", "Cells with UMI counts below this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 0, "nCount_RNA.low"),
+                    }}, 0, "nCount_RNA.low", false),
                     SeuratToolParameter.create("nCountRnaHigh", "Max UMI Count", "Cells with UMI counts above this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 20000, "nCount_RNA.high"),
+                    }}, 20000, "nCount_RNA.high", false),
                     SeuratToolParameter.create("nCountFeatureLow", "Min Feature Count", "Cells with unique feature totals below this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 200, "nFeature.low"),
+                    }}, 200, "nFeature.low", false),
                     SeuratToolParameter.create("nCountFeatureHigh", "Max Feature Count", "Cells with unique feature totals above this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
-                    }}, 5000, "nFeature.high"),
+                    }}, 5000, "nFeature.high", false),
                     SeuratToolParameter.create("pMitoLow", "Min Percent Mito", "Cells percent mitochondrial genes below this value will be discarded", "ldk-numberfield", new JSONObject(){{
                         put("minValue", 0);
                         put("maxValue", 1);
-                    }}, 0, "pMito.low"),
+                    }}, 0, "pMito.low", false),
                     SeuratToolParameter.create("pMitoHigh", "Max Percent Mito", "Cells percent mitochondrial genes above this value will be discarded", "ldk-numberfield", new JSONObject(){{
                         put("minValue", 0);
                         put("maxValue", 1);
-                    }}, 0.15, "pMito.high")
+                    }}, 0.15, "pMito.high", false)
                     ), null, null);
         }