--- a/ct_get_tool_perf_table.xml	Mon Apr 27 11:13:07 2020 -0400
+++ b/ct_get_tool_perf_table.xml	Wed Jun 17 12:31:30 2020 -0400
@@ -20,6 +20,9 @@
         #if $parallel
         --parallel "${parallel}"
         #end if
+        #if $include_sem_siml
+        --include-sem-siml "${include_sem_siml}"
+        #end if
         #if $barcode_col_ref
         --barcode-col-ref "${barcode_col_ref}"
         #end if
@@ -36,20 +39,21 @@
         --semantic-sim-metric "${semantic_sim_metric}" 
         #end if
 
-
          ]]></command>
     <inputs>
         <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
         <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
         <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
+        <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
         <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
-        <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
+        <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" />
+        <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
         <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
         <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" />
         <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" />
         <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
         <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" />
-        <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
+        <expand macro="sem_siml_options" />
     </inputs>
     <outputs>
          <data name="output_path" format="txt" />