--- a/kaks_analysis.xml	Thu Oct 05 14:25:47 2017 -0400
+++ b/kaks_analysis.xml	Mon Oct 23 13:56:14 2017 -0400
@@ -36,6 +36,10 @@
 #if str($comparison) == 'orthologs':
     --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
     --proteins_species_2 '$comparison_cond.proteins_species_2'
+    #set blast_option = $comparison_cond.blast_option
+    #if str($blast_option) == 'crbblast':
+        --crb_blast
+    #end if
 #end if
 #if str($options_type.options_type_selector) == 'advanced':
     #if str($set_min_coverage) == 'yes':
@@ -89,6 +93,10 @@
             <when value="orthologs">
                 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences for the second species" />
                 <param name="proteins_species_2" format="fasta" type="data" label="Protein sequences for the second species" />
+                <param name="blast_option" type="select" display="radio" label="Determine for cross-species orthologs using">
+                    <option value="blast" selected="true">reciprocal best BLAST</option>
+                    <option value="crbblast">conditional reciprocal best BLAST</option>
+                </param>
             </when>
         </conditional>
         <conditional name="options_type">
@@ -220,6 +228,12 @@
 
   - **Coding sequences for the second species** - coding sequence fasta file for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.  This option is required only for orthologous comparison.
   - **Protein sequences for the second species** - corresponding protein sequence fasta files for the second species either produced by the AssemblyPostProcessor tool or from an external source selected from your history.  This option is required only for orthologous comparison.
+
+  - **Determine for cross-species orthologs using** - select option for blast orthology.
+
+    - **reciprocal best BLAST** - use the default stringent reciprocal BLAST package for orthology assignment.
+    - **conditional reciprocal best BLAST** - use the CRB-BLAST package for orthology assignment which increases sensitivity to orthology comparisons and determines additional cross-species orthologs that are being left out by the defaul stringent reciprocal BLAST.
+
   - **Alignment coverage configuration** - select 'Yes' to set the minimum allowable alignment coverage length between homologous pairs.  PlantTribes uses global codon alignment match score to determine the pairwise alignment coverage.  By default, the match score is set to 0.5 if 'No' is selected.
 
     - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence.  Positions in the alignment corresponding to gaps are not considered.  The score is restricted to the range 0.3 - 1.0.