--- a/clearcut.xml	Fri Sep 08 13:08:06 2017 -0400
+++ b/clearcut.xml	Wed Feb 14 09:16:25 2018 -0500
@@ -7,37 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.infile" input.infile.dat &&
+## create symlinks to input datasets
+ln -s '$input.infile' input.infile.dat &&
 
-        echo 'clearcut(
-            #if $input.source == "dna":
-                fasta=input.infile.dat,
-                DNA=true,
-            #elif $input.source == "aa":
-                fasta=input.infile.dat,
-                protein=true,
-            #elif $input.source == "phylip":
-                phylip=input.infile.dat,
-            #end if
-            #if $matrixout == "true":
-                matrixout=matrixout.dist,
-            #end if
-            #if $seed:
-                seed=$seed,
-            #end if
-            ntrees=$ntrees,
-            norandom=$norandom,
-            shuffle=$shuffle,
-            expblen=$expblen,
-            expdist=$expdist,
-            neighbor=$neighbor
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'clearcut(
+    #if $input.source == "dna":
+        fasta=input.infile.dat,
+        DNA=true,
+    #elif $input.source == "aa":
+        fasta=input.infile.dat,
+        protein=true,
+    #elif $input.source == "phylip":
+        phylip=input.infile.dat,
+    #end if
+    #if $matrixout == "true":
+        matrixout=matrixout.dist,
+    #end if
+    #if $seed:
+        seed=$seed,
+    #end if
+    ntrees=$ntrees,
+    norandom=$norandom,
+    shuffle=$shuffle,
+    expblen=$expblen,
+    expdist=$expdist,
+    neighbor=$neighbor
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -47,23 +47,23 @@
                 <option value="phylip">Phylip Distance Matrix</option>
             </param>
             <when value="dna">
-                <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
+                <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
             </when>
             <when value="aa">
-                <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
+                <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
             </when>
             <when value="phylip">
-                <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param argument="phylip" name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
             </when>
         </conditional>
-        <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
-        <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
-        <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
-        <param name="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
-        <param name="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
-        <param name="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
-        <param name="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
-        <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
+        <param argument="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
+        <param argument="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
+        <param argument="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
+        <param argument="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
+        <param argument="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
+        <param argument="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
+        <param argument="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
+        <param argument="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -106,8 +106,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -125,7 +124,7 @@
 .. _clearcut: https://www.mothur.org/wiki/Clearcut
 
 v.1.20.0: Trivial upgrade to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>