--- a/deunique.seqs.xml	Tue Sep 05 17:10:53 2017 -0400
+++ b/deunique.seqs.xml	Tue Mar 20 22:14:50 2018 -0400
@@ -7,23 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$names" names.dat &&
+## create symlinks to input datasets
+ln -s '$fasta' fasta.dat &&
+ln -s '$names' names.dat &&
 
-         echo 'deunique.seqs(
-            #if $inputtype.intype == "countfile":
-                count=names.dat,
-            #else
-                name=names.dat,
-            #end if
-            fasta=fasta.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+ echo 'deunique.seqs(
+    #if $inputtype.intype == "countfile":
+        count=names.dat,
+    #else
+        name=names.dat,
+    #end if
+    fasta=fasta.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
@@ -36,9 +36,12 @@
                 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
             </when>
             <when value="countfile">
-                <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/>
+                <param name="names" type="data" format="mothur.count_table" label="provide a count table"
+                    help="A counts table will generate a new faste file containing all the sequences.
+                    If the file contains group information, a group file will also be created."/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -54,6 +57,7 @@
             <param name="intype" value="namesfile"/>
             <param name="names" value="amazon.unique.names"/>
             <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test count file input with group file output -->
@@ -62,6 +66,7 @@
             <param name="names" value="amazon_withgroups.count_table"/>
             <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
             <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test count file input without group file output -->
@@ -70,11 +75,11 @@
             <param name="names" value="amazon.count_table"/>
             <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
             <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -87,7 +92,6 @@
 
 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>