--- a/corr.axes.xml	Tue Sep 05 17:09:59 2017 -0400
+++ b/corr.axes.xml	Tue Mar 20 22:08:33 2018 -0400
@@ -8,38 +8,38 @@
     <expand macro="version_command"/>
 
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        #if $input.source == "shared":
-            ln -s "$input.otu" input.otu.dat &&
-        #else
-            ln -s "$input.metadata" input.metadata.dat &&
-        #end if
+## create symlinks to input datasets
+#if $input.source == "shared":
+    ln -s '$input.otu' input.otu.dat &&
+#else
+    ln -s '$input.metadata' input.metadata.dat &&
+#end if
 
-        echo 'corr.axes(
-            #if $input.source == "shared":
-                #if $input.otu.is_of_type("mothur.relabund"):
-                    relabund=input.otu.dat,
-                #elif $input.otu.is_of_type("mothur.shared"):
-                    shared=input.otu.dat,
-                #end if
-                #if $input.label:
-                    label=$input.label,
-                #end if
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-            #else:
-                metadata=input.metadata.dat,
-            #end if
-            method=$method,
-            axes=$axes,
-            numaxes=$numaxes
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'corr.axes(
+    #if $input.source == "shared":
+        #if $input.otu.is_of_type("mothur.relabund"):
+            relabund=input.otu.dat,
+        #elif $input.otu.is_of_type("mothur.shared"):
+            shared=input.otu.dat,
+        #end if
+        #if $input.label:
+            label=$input.label,
+        #end if
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+    #else:
+        metadata=input.metadata.dat,
+    #end if
+    method=$method,
+    axes=$axes,
+    numaxes=$numaxes
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/>
@@ -60,7 +60,8 @@
                 </param>
             </when>
             <when value="metadata">
-                <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values" help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/>
+                <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values"
+                    help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/>
             </when>
         </conditional>
         <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
@@ -69,6 +70,7 @@
                 <option value="kendall">kendall</option>
         </param>
         <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -80,6 +82,7 @@
             <param name="source" value="shared"/>
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with metadata file -->
@@ -87,6 +90,7 @@
             <param name="source" value="metadata"/>
             <param name="metadata" value="amazon.metadata" ftype="tabular"/>
             <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with relabund file and label and group select -->
@@ -96,11 +100,11 @@
             <param name="groups" value="forest,pasture"/>
             <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
             <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -112,7 +116,6 @@
 
 v.1.21.0: Updated to mothur 1.33
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>