--- a/anosim.xml	Tue Sep 05 16:58:18 2017 -0400
+++ b/anosim.xml	Tue Mar 20 22:09:48 2018 -0400
@@ -7,35 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$design" design.dat &&
+## create symlinks to input datasets
+ln -s '$phylip' phylip.dat &&
+ln -s '$design' design.dat &&
 
-        echo 'anosim(
-            phylip=dist.dat,
-            iters=$iters,
-            alpha=$alpha,
-            design=design.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'anosim(
+    phylip=phylip.dat,
+    iters=$iters,
+    alpha=$alpha,
+    design=design.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
-        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
-        <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
-        <param name="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision (default 0.05)"/>
-        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
+        <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param argument="design" type="data" format="tabular" label="design - assign groups to new grouping"
+            help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
+        <param argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/>
+        <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="anosim" format="tabular" from_work_dir="dist.anosim" label="${tool.name} on ${on_string}: anosim"/>
+        <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/>
     </outputs>
     <tests>
         <test>
-            <param name="dist" value="amazon.dist"/>
+            <param name="phylip" value="amazon.dist"/>
             <param name="design" value="amazon.design"/>
             <output name="anosim" ftype="tabular">
                 <assert_contents>
@@ -43,11 +45,11 @@
                     <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -70,7 +72,6 @@
 .. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _anosim: https://www.mothur.org/wiki/Anosim
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>