--- a/ct_get_consensus_outputs.xml	Mon Apr 27 11:12:14 2020 -0400
+++ b/ct_get_consensus_outputs.xml	Wed Jun 17 12:29:44 2020 -0400
@@ -16,9 +16,15 @@
         #if $tool_table
         --tool-table "${tool_table}"
         #end if
+        #if $include-sem-siml
+        --include-sem-siml "${include_sem_siml}"
+        #end if
         #if $parallel
         --parallel "${parallel}"
         #end if
+        #if $sort_by_agg_score
+        --sort-by-agg-score "${sort_by_agg_score}"
+        #end if
         #if $exclusions
         --exclusions "${exclusions}"
         #end if
@@ -30,10 +36,13 @@
         <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" />
         <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" />
         <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
+        <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
+        <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="boolean" name="sort_by_agg_score" label="Sort by aggregated score" checked="true" help="Should the cells be ordered by aggregated score?" />
         <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
         <param type="data" name="lab_cl_mapping" format="rdata" label="cl terms mapping" help="Label - CL term mapping" />
-        <param type="data" name="ontology_graph" format="obo" label="Ontology graph" help="Ontology graph to run similairty calculations" />
-        <param type="text" name="semantic_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
+        <param type="data" name="ontology_graph" format="obo" label="Ontology graph" optional="true" help="Ontology graph to run similairty calculations" />
+        <expand macro="sem_siml_options" />
     </inputs>
     <outputs>
         <data name="summary_table_output_path" format="txt" />