--- a/pairwise.seqs.xml	Tue Sep 05 17:06:35 2017 -0400
+++ b/pairwise.seqs.xml	Tue Mar 20 21:55:43 2018 -0400
@@ -7,35 +7,35 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
 
-        echo 'pairwise.seqs(
-            fasta=fasta.dat,
-            align=$align,
-            #if $calc:
-                calc=$calc,
-            #end if
-            $countends
-            #if float($cutoff) > 0.0:
-                cutoff=$cutoff,
-            #end if
-            #if $scoring.setby == "user":
-                match=$scoring.match,
-                mismatch=$scoring.mismatch,
-                gapopen=$scoring.gapopen,
-                gapextend=$scoring.gapextend,
-            #end if
-            #if $output:
-                output=$output,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'pairwise.seqs(
+    fasta=fasta.dat,
+    align=$align,
+    #if $calc:
+        calc=$calc,
+    #end if
+    $countends
+    #if float($cutoff) > 0.0:
+        cutoff=$cutoff,
+    #end if
+    #if $scoring.setby == "user":
+        match=$scoring.match,
+        mismatch=$scoring.mismatch,
+        gapopen=$scoring.gapopen,
+        gapextend=$scoring.gapextend,
+    #end if
+    #if $output:
+        output=$output,
+    #end if
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
@@ -70,6 +70,7 @@
             <option value="lt">Phylip formatted Lower Triangle Matrix</option>
             <option value="square">Phylip formatted Square Matrix</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -89,6 +90,7 @@
             <param name="cutoff" value="0.0"/>
             <param name="setby" value="default"/>
             <param name="output" value=""/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
             <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
         </test>
@@ -104,12 +106,12 @@
                 <param name="gapopen" value="-2"/>
                 <param name="gapextend" value="-1"/>
             <param name="output" value="lt"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
             <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -123,7 +125,6 @@
 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>