--- a/summary.seqs.xml	Tue Sep 05 17:16:26 2017 -0400
+++ b/summary.seqs.xml	Tue Mar 20 21:59:09 2018 -0400
@@ -7,31 +7,32 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'summary.seqs(
-            fasta=fasta.dat,
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'summary.seqs(
+    fasta=fasta.dat,
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #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,mothur.align" label="fasta - Dataset"/>
         <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -41,23 +42,25 @@
         <test>
             <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
             <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test names input -->
             <param name="fasta" value="amazon.unique.fasta"/>
             <param name="name" value="amazon.names"/>
             <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test count input -->
             <param name="fasta" value="amazon.unique.fasta"/>
             <param name="count" value="amazon.count_table"/>
             <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -67,7 +70,7 @@
 
 
 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>