--- a/nmds.xml	Tue Sep 05 17:04:36 2017 -0400
+++ b/nmds.xml	Tue Mar 20 22:12:24 2018 -0400
@@ -7,31 +7,31 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$dist" dist.dat &&
-        ln -s "$axes" axes.dat &&
+## create symlinks to input datasets
+ln -s '$dist' dist.dat &&
+ln -s '$axes' axes.dat &&
 
-        echo 'nmds(
-            phylip=dist.dat
-            #if $axes:
-                ,axes=axes.dat
-            #end if
-            ,mindim=$mindim
-            #if $maxdim >= $mindim:
-                ,maxdim=$maxdim
-            #end if
-            ,iters=$iters
-            ,maxiters=$maxiters
+echo 'nmds(
+    phylip=dist.dat
+    #if $axes:
+        ,axes=axes.dat
+    #end if
+    ,mindim=$mindim
+    #if $maxdim >= $mindim:
+        ,maxdim=$maxdim
+    #end if
+    ,iters=$iters
+    ,maxiters=$maxiters
 
-            ## Mothur can't cope with scientific notation
-            #set epsilon_decimal = "{:.12f}".format(float($epsilon))
-            ,epsilon=$epsilon_decimal
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+    ## Mothur can't cope with scientific notation
+    #set epsilon_decimal = "{:.12f}".format(float($epsilon))
+    ,epsilon=$epsilon_decimal
+)'
+| 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"/>
@@ -41,6 +41,7 @@
         <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
         <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
         <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -60,11 +61,11 @@
             <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
             <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
             <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -78,7 +79,7 @@
 .. _nmds: https://www.mothur.org/wiki/Nmds
 
 v1.20.0: Updated to mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>