--- 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" />

--- a/ct_macros.xml	Mon Apr 27 11:12:14 2020 -0400
+++ b/ct_macros.xml	Wed Jun 17 12:29:44 2020 -0400
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.0.0</token>
+    <token name="@TOOL_VERSION@">1.1.0</token>
     <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.8">cell-types-analysis</requirement>
+        <requirement type="package" version="0.1.1">cell-types-analysis</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -18,6 +18,22 @@
 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
 0.0.5+galaxy1: Standardise input/output format into .txt. 
     ]]></token>
+    <xml name="sem_siml_options">
+      <param type="select" name="sem_siml_metric" label="Semantic similarity metric"  help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">
+            <option value="lin" selected="true">lin</option>
+            <option value="jaccard">jaccard</option>
+            <option value="jc_norm">jc_norm</option>
+            <option value="schlicker">schlicker</option>
+            <option value="edge_resnik">edge_resnik</option>
+            <option value="sim">sim</option>
+            <option value="edge_leachod">edge_leachod</option>
+            <option value="edge_slimani">edge_slimani</option>
+            <option value="edge_wupalmer">edge_wupalmer</option>
+            <option value="edge_rada_lca">edge_rada_lca</option>
+            <option value="edge_li">edge_li</option>
+            <option value="resnik">resnik</option>
+        </param>
+    </xml>
     <xml name="citations">
       <citations>
         <citation type="bibtex">