--- a/macros.xml	Tue Dec 04 17:17:41 2018 -0500
+++ b/macros.xml	Wed Dec 05 14:37:17 2018 -0500
@@ -6,6 +6,24 @@
             <yield/>
         </requirements>
     </xml>
+    <xml name="ONTOLOGY_ARGS">
+        <conditional name="ontology_args">
+            <param name="ontology" type="select" label="Ontology">
+                <option value="go">GO Gene Ontology (column named 'go')</option>
+                <option value="ec">EC Enzyme Commission (column named 'ec')</option>
+                <option value="cog">COG (column named 'cog')</option>
+            </param>
+            <when value="go">
+                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
+            </when>
+            <when value="ec">
+                <!-- do nothing -->
+            </when>
+            <when value="cog">
+                <!-- do nothing -->
+            </when>
+        </conditional>
+    </xml>
     <xml name="FUNC_FILE">
         <param argument="--func_file" type="data" format="tabular" label="Functional file"
             help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/>
@@ -50,7 +68,7 @@
     </token>
     <token name="@DB_DIR@"><![CDATA[
         #if $db_dir.db_loc == 'auto':
-            #if $mode_args.mode == 'taxfn'
+            #if $mode_args.mode == 'ft'
                 --ft_func_data_dir data
                 --ft_tax_data_dir  data
             #else
@@ -85,6 +103,27 @@
             --samps samp_file.tab
             --mode '$mode_args.mode'
             #if $mode_args.mode == 'f'
+                --ontology='$mode_args.ontology_args.ontology'
+                #if $mode_args.ontology_args.ontology == 'go'
+                    #if $mode_args.ontology_args.slim_down
+                        --slim_down
+                    #end if
+                #end if
+            #end if
+            #if $mode_args.mode == 'ft'
+                --ontology='$mode_args.ontology_args.ontology'
+                #if $mode_args.ontology_args.ontology == 'go'
+                    #if $mode_args.ontology_args.slim_down
+                        --slim_down
+                    #end if
+                #end if
+            #end if
+    ]]>
+    </token>
+    <token name="@EXPAND_PARAMS@"><![CDATA[
+            --samps samp_file.tab
+            --mode '$mode_args.mode'
+            #if $mode_args.mode == 'f'
                 --func_file='$mode_args.func_file'
                 --func_colname='$mode_args.func_colname'
                 --pep_colname_func='$mode_args.pep_colname_func'
@@ -104,7 +143,12 @@
                 --func_file='$mode_args.func_file'
                 --func_colname='$mode_args.func_colname'
                 --pep_colname_func='$mode_args.pep_colname_func'
-                --ontology=$mode_args.ontology
+                --ontology='$mode_args.ontology_args.ontology'
+                #if $mode_args.ontology_args.ontology == 'go'
+                    #if $mode_args.ontology_args.slim_down
+                        --slim_down
+                    #end if
+                #end if
                 --tax_file='$mode_args.tax_file'
                 --tax_colname='$mode_args.tax_colname'
                 --pep_colname_tax='$mode_args.pep_colname_tax'
@@ -112,6 +156,7 @@
             #end if
     ]]>
     </token>
+
     <xml name="SAMPS">
         <conditional name="samps_args">
             <param argument="samps_src" type="select" label="Samples">
@@ -138,29 +183,33 @@
                 <option value="ft">Functional-taxonomic interaction analysis</option>
             </param>
             <when value="f">
+                <expand macro="ONTOLOGY_ARGS"/>
+            </when>
+            <when value="t">
+            </when>
+            <when value="ft">
+                <expand macro="ONTOLOGY_ARGS"/>
+            </when>
+        </conditional>
+        <expand macro="SAMPS"/>
+    </xml>
+    <xml name="expand_params">
+        <conditional name="mode_args">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="f">Functional analysis</option>
+                <option value="t">Taxonomic analysis</option>
+                <option value="ft">Functional-taxonomic interaction analysis</option>
+            </param>
+            <when value="f">
                 <expand macro="FUNC_FILE"/>
-                <conditional name="ontology_args">
-                    <param name="ontology" type="select" label="Ontology">
-                        <option value="go">GO Gene Ontology (column named 'go')</option>
-                        <option value="ec">EC Enzyme Commission (column named 'ec')</option>
-                        <option value="cog">COG (column named 'cog')</option>
-                    </param>
-                    <when value="go">
-                        <param argument="--slim_down" type="boolean" label="Use slim GO"/>
-                    </when>
-                    <when value="ec">
-                        <!-- do nothing -->
-                    </when>
-                    <when value="cog">
-                        <!-- do nothing -->
-                    </when>
-                </conditional>
+                <expand macro="ONTOLOGY_ARGS"/>
             </when>
             <when value="t">
                 <expand macro="TAX_FILE"/>
             </when>
             <when value="ft">
                 <expand macro="FUNC_FILE"/>
+                <expand macro="ONTOLOGY_ARGS"/>
                 <expand macro="TAX_FILE"/>
                 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
                     <option value="species">species</option>
@@ -175,6 +224,7 @@
         </conditional>
         <expand macro="SAMPS"/>
     </xml>
+
     <xml name="output_samples_choice">
         <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/>
     </xml>