--- a/summary.tax.xml	Tue Sep 05 16:54:59 2017 -0400
+++ b/summary.tax.xml	Tue Mar 20 22:24:38 2018 -0400
@@ -7,37 +7,33 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$tax.taxonomy" tax.taxonomy.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$count" count.dat &&
-        #if $reftax.source2:
-            ln -s "$reftax.reftaxonomy" myreftax.taxonomy &&
-            ln -s "$sum" myreftax.tree.sum &&
-        #end if
+## create symlinks to input datasets
+ln -s '$tax.taxonomy' tax.taxonomy.dat &&
+ln -s '$name' name.dat &&
+ln -s '$group' group.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'summary.tax(
-            taxonomy=tax.taxonomy.dat,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $group:
-                group=group.dat,
-            #end if
-            #if $reftax.source2:
-                reftaxonomy=myreftax.taxonomy,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            relabund=$relabund
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'summary.tax(
+    taxonomy=tax.taxonomy.dat,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $group:
+        group=group.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    relabund=$relabund,
+    threshold=$threshold,
+    output=$output,
+    printlevel=$printlevel
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="tax">
@@ -56,50 +52,49 @@
         </conditional>
         <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
         <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
-        <conditional name="reftax">
-            <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
-                <option value="" selected="true">Selection is Optional</option>
-                <option value="hist">History</option>
-                <option value="ref">Cached Reference</option>
-            </param>
-            <when value="ref">
-                <param name="reftaxonomy" 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="reftaxonomy" 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>
-            <when value=""/>
-        </conditional>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
-        <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
+        <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false"
+            label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
+        <param name="threshold" type="integer" value="0" min="0" label="threshold- specify a cutoff for the taxonomy file"
+            help="Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus.
+            This feature is similar to adjusting the cutoff in classify.seqs"/>
+        <expand macro="param-output"/>
+        <expand macro="param-printlevel"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="taxsummary" format="mothur.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
+        <data name="taxsummary" format="mothur.tax.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
     </outputs>
     <tests>
         <test>
             <param name="source" value="hist"/>
             <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
-            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
+            <output name="taxsummary" ftype="mothur.tax.summary">
+                <assert_contents>
+                    <expand macro="test-taxsummary-format"/>
+                    <has_text text="Root"/>
+                    <has_text text="Bifidobacterium"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <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"/>
-            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
+            <output name="taxsummary" ftype="mothur.tax.summary">
+                <assert_contents>
+                    <expand macro="test-taxsummary-format"/>
+                    <has_text text="Root"/>
+                    <has_text text="Bifidobacterium"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -108,7 +103,7 @@
 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.
 
 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>