--- a/kaks_analysis.xml	Wed Mar 01 11:16:57 2017 -0500
+++ b/kaks_analysis.xml	Wed Mar 01 13:40:40 2017 -0500
@@ -13,6 +13,7 @@
     </stdio>
     <command>
         <![CDATA[
+            #set output_dir = 'kaksAnalysis_dir'
             #set comparison = $comparison_cond.comparison
             #if str($options_type.options_type_selector) == 'advanced':
                 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
@@ -44,13 +45,25 @@
                     --max_ks $fit_components_cond.max_ks
                 #end if
             #end if
+            && mv $output_dir/species1.fna '$output_species1_fna'
+            && mv $output_dir/species1.faa '$output_species1_faa'
+            #if str($comparison) == 'orthologs':
+                && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
+            #end if
+            #if str($comparison) == 'orthologs':
+                && 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 $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
+            #end if
+            && mv $output_dir/*.rbhb '$output_rbhb'
+            && mv $output_dir/*.kaks '$output_kaks'
+            #if str($fit_components) == 'yes':
+                && mv $output_dir/*.components '$output_components'
+            #end if
         ]]>
     </command>
     <inputs>
-        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
-            <options from_data_table="plant_tribes_scaffolds" />
-            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
-        </param>
         <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
         <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
         <conditional name="comparison_cond">
@@ -64,6 +77,10 @@
                 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
             </when>
         </conditional>
+        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
+            <options from_data_table="plant_tribes_scaffolds" />
+            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table."/>
+        </param>
         <conditional name="options_type">
             <param name="options_type_selector" type="select" label="Options Configuration">
                 <option value="basic" selected="true">Basic</option>
@@ -99,9 +116,28 @@
         </conditional>
     </inputs>
     <outputs>
-        <collection name="ks_files" type="list">
-            <discover_datasets pattern="__name__" directory="kaksAnalysis_dir" visible="false" ext="fasta" />
-        </collection>
+        <data name="output_species1_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}" />
+        <data name="output_species1_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}" />
+        <data name="output_species2_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}">
+            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
+        </data>
+        <data name="output_species2_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}">
+            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
+        </data>
+        <data name="output_species1_paralog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
+            <filter>comparison_cond['comparison'] == 'paralogs'</filter>
+        </data>
+        <data name="output_species1_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
+            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
+        </data>
+        <data name="output_species2_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
+            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
+        </data>
+        <data name="output_rbhb" format="tabular" label="KaKs analysis (paralogous pairs) on ${on_string}" />
+        <data name="output_kaks" format="tabular" label="KaKs analysis on ${on_string}" />
+        <data name="output_components" format="tabular" label="KaKs analysis (significant components in the ks distribution) on ${on_string}">
+            <filter>options_type[options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes</filter>
+        </data>
     </outputs>
     <tests>
         <test>