--- a/classify.otu.xml	Tue Sep 05 16:05:02 2017 -0400
+++ b/classify.otu.xml	Wed Feb 14 09:34:34 2018 -0500
@@ -7,93 +7,77 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$tax.taxonomy" tax.taxonomy.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
-        ln -s "$group" group.dat &&
-        #if $reftax.source2:
-            ln -s "$reftax.taxonomy" myreftax.taxonomy &&
-            ln -s "$sum" myreftax.tree.sum &&
-        #end if
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$tax.taxonomy' tax.taxonomy.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
+ln -s '$group' group.dat &&
 
-        echo 'classify.otu(
-            list=otu.dat,
-            taxonomy=tax.taxonomy.dat,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            #if $reftax.source2:
-                reftaxonomy=myreftax.taxonomy,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $group:
-                group=group.dat,
-            #end if
-            basis=$basis,
-            probs=$probs,
-            persample=$persample,
-            cutoff=$cutoff
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'classify.otu(
+    list=otu.dat,
+    taxonomy=tax.taxonomy.dat,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $group:
+        group=group.dat,
+    #end if
+    basis=$basis,
+    probs=$probs,
+    persample=$persample,
+    cutoff=$cutoff,
+    relabund=$relabund,
+    output=$output,
+    printlevel=$printlevel
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="otu" type="data" format="mothur.list" label="list - OTU List "/>
-        <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
+        <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List "/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - used to represent the number of duplicate sequences for a given representative sequence"/>
         <conditional name="tax">
             <param name="source" type="select" label="Select Taxonomy from" help="">
                 <option value="hist">History</option>
                 <option value="ref">Cached Reference</option>
             </param>
             <when value="ref">
-                <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
+                <param argument="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference">
                     <options from_data_table="mothur_taxonomy"/>
                 </param>
             </when>
             <when value="hist">
-                <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
+                <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
             </when>
         </conditional>
-        <conditional name="reftax">
-            <param name="source2" type="select" label="Select Reference Taxonomy used in Classify.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
-                <option value="">Selection is Optional</option>
-                <option value="hist">History</option>
-                <option value="ref">Cached Reference</option>
-            </param>
-            <when value=""/>
-            <when value="ref">
-                <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
-                    <options from_data_table="mothur_taxonomy"/>
-                </param>
-                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
-            </when>
-            <when value="hist">
-                <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
-                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
-            </when>
-        </conditional>
-        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+        <param argument="label" type="select" label="label - OTU Labels" multiple="true">
             <expand macro="labeloptions"/>
         </param>
-        <param name="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
-        <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
-        <param name="basis" type="select" label="basis - Summary file gives numbers of" help="">
+        <param argument="cutoff" type="integer" value="60" min="0" max="100" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
+        <param argument="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
+        <param argument="basis" type="select" label="basis - Summary file gives numbers of" help="">
             <option value="otu">OTU</option>
             <option value="sequence">sequence</option>
         </param>
-        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
-        <param name="persample" type="boolean" falsevalue="false" truevalue="true" checked="false" label="persample - allows you to find a consensus taxonomy for each group. default=f"/>
+        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
+        <param argument="persample" type="boolean" falsevalue="false" truevalue="true" checked="false"
+            label="persample - allows you to find a consensus taxonomy for each group"
+            help="default false"/>
+        <param argument="relabund" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Relative abundance values?"
+            help="use relative abundances rather than raw abundances for the tax.summary file"/>
+        <expand macro="param-output"/>
+        <expand macro="param-printlevel"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -110,27 +94,45 @@
             <param name="source" value="hist"/>
             <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <output_collection name="taxonomies" count="36">
-                <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/>
+                <element name="0.18" ftype="mothur.cons.taxonomy">
+                    <assert_contents>
+                        <expand macro="test-taxonomy-format"/>
+                        <has_text text="Otu01"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="taxsummaries" count="36">
-                <element name="0.18" md5="bd5613b544a70c5c19f21a3d6602d926" ftype="mothur.tax.summary"/>
+                <element name="0.18" ftype="mothur.tax.summary">
+                    <assert_contents>
+                        <expand macro="test-taxsummary-format"/>
+                        <has_text text="Root"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with reftaxonomy and names file and label select -->
+        <test><!-- test with names file and label select -->
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="name" value="amazon1.names" ftype="mothur.names"/>
             <param name="source" value="hist"/>
             <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
-            <param name="source2" value="hist"/>
-            <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
             <param name="label" value="unique,0.05,0.18"/>
             <output_collection name="taxonomies" count="3">
-                <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/>
+                <element name="0.18" ftype="mothur.cons.taxonomy">
+                    <assert_contents>
+                        <expand macro="test-taxonomy-format"/>
+                        <has_text text="Otu01"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="taxsummaries" count="3">
-                <element name="0.18" md5="115769aa33dcfd121dd945a40ea11dcb" ftype="mothur.tax.summary"/>
+                <element name="0.18" ftype="mothur.tax.summary">
+                    <assert_contents>
+                        <expand macro="test-taxsummary-format"/>
+                        <has_text text="Root"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
@@ -141,10 +143,20 @@
             <param name="label" value="unique,0.05,0.18"/>
             <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <output_collection name="taxonomies" count="3">
-                <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/>
+                <element name="0.18" ftype="mothur.cons.taxonomy">
+                    <assert_contents>
+                        <expand macro="test-taxonomy-format"/>
+                        <has_text text="Otu01"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="taxsummaries" count="3">
-                <element name="0.18" md5="bd5613b544a70c5c19f21a3d6602d926" ftype="mothur.tax.summary"/>
+                <element name="0.18" ftype="mothur.tax.summary">
+                    <assert_contents>
+                        <expand macro="test-taxsummary-format"/>
+                        <has_text text="Root"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
@@ -155,16 +167,25 @@
             <param name="label" value="unique,0.05,0.18"/>
             <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
             <output_collection name="taxonomies" count="3">
-                <element name="0.18" md5="69a80ebaeb368d4944aa95ce120c6643" ftype="mothur.cons.taxonomy"/>
+                <element name="0.18" ftype="mothur.cons.taxonomy">
+                    <assert_contents>
+                        <expand macro="test-taxonomy-format"/>
+                        <has_text text="Otu01"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="taxsummaries" count="3">
-                <element name="0.18" md5="fe038e7670fbc5d68c1f5bb79d8ef4ac" ftype="mothur.tax.summary"/>
+                <element name="0.18" ftype="mothur.tax.summary">
+                    <assert_contents>
+                        <expand macro="test-taxsummary-format"/>
+                        <has_text text="Root"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -177,7 +198,7 @@
 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
 
 v1.21.0: Updated to use Mothur 1.33. Added count parameter (1.28.0) and persample parameter (1.29.0)
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>