--- a/split.groups.xml	Tue Sep 05 17:02:15 2017 -0400
+++ b/split.groups.xml	Tue Mar 20 22:23:21 2018 -0400
@@ -7,30 +7,30 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$name" name.dat &&
-        ln -s "$count" count.dat &&
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$group" group.dat &&
+## create symlinks to input datasets
+ln -s '$name' name.dat &&
+ln -s '$count' count.dat &&
+ln -s '$fasta' fasta.dat &&
+ln -s '$group' group.dat &&
 
-        echo 'split.groups(
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            fasta=fasta.dat,
-            group=group.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'split.groups(
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    fasta=fasta.dat,
+    group=group.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
@@ -42,6 +42,7 @@
             </options>
         </param>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -58,11 +59,11 @@
                 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
                 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -73,7 +74,7 @@
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _name: https://www.mothur.org/wiki/Name_file
 .. _split.groups: https://www.mothur.org/wiki/Split.groups
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>