--- a/kaks_analysis.xml	Mon Oct 23 13:56:14 2017 -0400
+++ b/kaks_analysis.xml	Tue Oct 24 08:40:46 2017 -0400
@@ -36,8 +36,7 @@
 #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':
+    #if str($comparison_cond.blast_option) == 'crbblast':
         --crb_blast
     #end if
 #end if
@@ -68,11 +67,11 @@
 && mv $output_dir/species1.fna '$output_species1_fna'
 && mv $output_dir/species1.faa '$output_species1_faa'
 #if str($comparison) == 'paralogs':
-    && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
+    && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_para_ortho'
 #else:
     && mv $output_dir/species2.faa '$output_species2_faa'
     && mv $output_dir/species2.fna '$output_species2_fna'
-    && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
+    && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_para_ortho'
     && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
 #end if
 && mv $output_dir/*.rbhb '$output_rbhb'
@@ -174,26 +173,21 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}" />
-        <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}" />
-        <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences) on ${on_string}">
+        <data name="output_species1_fna" format="fasta" label="${tool.name} (coding sequences species1) on ${on_string}" />
+        <data name="output_species1_faa" format="fasta" label="${tool.name} (amino acids species1) on ${on_string}" />
+        <data name="output_species2_fna" format="fasta" label="${tool.name} (coding sequences species2) on ${on_string}">
             <filter>comparison_cond['comparison'] == 'orthologs'</filter>
         </data>
-        <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids) on ${on_string}">
+        <data name="output_species2_faa" format="fasta" label="${tool.name} (amino acids species2) on ${on_string}">
             <filter>comparison_cond['comparison'] == 'orthologs'</filter>
         </data>
-        <data name="output_species1_paralog" format="tabular" label="${tool.name} (blastn results) on ${on_string}">
-            <filter>comparison_cond['comparison'] == 'paralogs'</filter>
-        </data>
-        <data name="output_species1_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}">
+        <data name="output_species1_para_ortho" format="tabular" label="${tool.name} (blastn results species1 vs species2) on ${on_string}"/>
+        <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results species2 vs species1) on ${on_string}">
             <filter>comparison_cond['comparison'] == 'orthologs'</filter>
         </data>
-        <data name="output_species2_ortholog" format="tabular" label="${tool.name} (blastn results) on ${on_string}">
-            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
-        </data>
-        <data name="output_rbhb" format="tabular" label="${tool.name} (paralogous pairs) on ${on_string}" />
-        <data name="output_kaks" format="tabular" label="${tool.name} on ${on_string}" />
-        <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the ks distribution) on ${on_string}">
+        <data name="output_rbhb" format="tabular" label="${tool.name} (orthologous pairs) on ${on_string}" />
+        <data name="output_kaks" format="tabular" label="${tool.name} (KaKs distribution) on ${on_string}" />
+        <data name="output_components" format="ptkscmp" label="${tool.name} (significant components in the KaKs distribution) on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter>
         </data>
     </outputs>
@@ -204,7 +198,7 @@
             <param name="non_commercial_use" value="True"/>
             <output name="output_species1_fna" file="species1_cds.fasta" ftype="fasta" compare="contains"/>
             <output name="output_species1_faa" file="species1_pep.fasta" ftype="fasta" compare="contains"/>
-            <output name="output_species1_paralog" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_species1_para_ortho" file="output_blastn_results1.tabular" ftype="tabular" compare="contains"/>
             <output name="output_rbhb" file="output_paralogous_pairs.tabular" ftype="tabular"/>
             <output name="output_kaks" file="output1.tabular" ftype="tabular"/>
         </test>