--- a/pick_closed_reference_otus.xml	Mon Jul 10 16:46:01 2017 -0400
+++ b/pick_closed_reference_otus.xml	Sat Aug 05 07:30:47 2017 -0400
@@ -1,43 +1,43 @@
-<tool id="qiime_pick_closed_reference_otus" name="Perform closed-reference OTU picking" version="@WRAPPER_VERSION@.0">
-    <description></description>
+<tool id="qiime_pick_closed_reference_otus" name="Closed-reference OTU picking" version="@WRAPPER_VERSION@.0">
+    <description> Shotgun UniFrac workflow (pick_closed_reference_otus)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>pick_closed_reference_otus.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        pick_closed_reference_otus.py
-            --input_fp '$input_fp'
-            --output_dir otus
-            #if str( $ref_seq.selector ) == 'history'
-                #set $ref = $ref_seq.reference_fp
-            #else
-                #set $ref = $ref_seq.reference_fp.fields.path
-            #end if
-            --reference_fp '$ref'
-            #if str( $taxonomy.selector ) == 'taxonomy_map'
-                #if str( $taxonomy.taxo_map.selector ) == 'history'
-                    #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp
-                #else
-                    #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path
-                #end if
-                --taxonomy_fp '$taxonomy'
-            #else if str( $taxonomy.selector ) == 'assign_taxonomy'
-                --assign_taxonomy
-            #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment'
-                --suppress_taxonomy_assignment
-            #end if
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
+pick_closed_reference_otus.py
+    --input_fp '$input_fp'
+    --output_dir otus
+    #if str( $ref_seq.selector ) == 'history'
+        #set $ref = $ref_seq.reference_fp
+    #else
+        #set $ref = $ref_seq.reference_fp.fields.path
+    #end if
+    --reference_fp '$ref'
+    #if str( $taxonomy.selector ) == 'taxonomy_map'
+        #if str( $taxonomy.taxo_map.selector ) == 'history'
+            #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp
+        #else
+            #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path
+        #end if
+        --taxonomy_fp '$taxonomy'
+    #else if str( $taxonomy.selector ) == 'assign_taxonomy'
+        --assign_taxonomy
+    #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment'
+        --suppress_taxonomy_assignment
+    #end if
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
     ]]></command>
     <inputs>
         <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/>
         <conditional name="ref_seq">
             <param name="selector" type="select" label="Reference sequences to query">
-                <option value="cached" selected="True">Public databases</option>
+                <option value="cached" selected="true">Public databases</option>
                 <option value="history">Databases from your history</option>
             </param>
             <when value="cached">
@@ -50,8 +50,8 @@
             </when>
         </conditional>
         <conditional name="taxonomy">
-            <param name="selector" type="select"  label="Assign taxonomy?">
-                <option value="taxonomy_map" selected="True">Assign taxonomy using a taxonomy map</option>
+            <param name="selector" type="select" label="Assign taxonomy?">
+                <option value="taxonomy_map" selected="true">Assign taxonomy using a taxonomy map</option>
                 <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option>
                 <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option>
             </param>
@@ -75,7 +75,7 @@
             <when value="suppress_taxonomy_assignment"/>
         </conditional>
         <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
-        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
     </inputs>
     <outputs>
         <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/>