--- a/make.shared.xml	Tue Sep 05 16:59:06 2017 -0400
+++ b/make.shared.xml	Tue Mar 20 21:57:06 2018 -0400
@@ -7,43 +7,43 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$intype.otu" intype_otu.dat &&
-        #if $intype.infile == "otulist":
-            ln -s "$intype.group" intype_group.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$intype.otu' intype_otu.dat &&
+#if $intype.infile == "otulist":
+    ln -s '$intype.group' intype_group.dat &&
+#end if
 
-        echo 'make.shared(
-            #if $intype.infile == "biom":
-                biom=intype_otu.dat
-            #else
-                #if $intype.group.is_of_type("mothur.groups"):
-                    group=intype_group.dat,
-                #elif $intype.group.is_of_type("mothur.count_table"):
-                    count=intype_group.dat,
-                #end if
-                #if $intype.label:
-                    label=${ str($intype.label).replace(",","-") },
-                #end if
-                #if $intype.groups:
-                    groups=${ str($intype.groups).replace(",","-") },
-                #end if
-                list=intype_otu.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log &&
+echo 'make.shared(
+    #if $intype.infile == "biom":
+        biom=intype_otu.dat
+    #else
+        #if $intype.group.is_of_type("mothur.groups"):
+            group=intype_group.dat,
+        #elif $intype.group.is_of_type("mothur.count_table"):
+            count=intype_group.dat,
+        #end if
+        #if $intype.label:
+            label=${ str($intype.label).replace(",","-") },
+        #end if
+        #if $intype.groups:
+            groups=${ str($intype.groups).replace(",","-") },
+        #end if
+        list=intype_otu.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log &&
 
-        ## move output files to correct destination
-        mv mothur.*.logfile "$logfile" &&
-        #if $intype.infile == 'otulist' and $intype.groups:
-            mv intype_otu*.groups "$groupout"
-        #else
-            mv intype_otu*.shared "$shared"
-        #end if
+## move output files to correct destination
+mv mothur.*.logfile "$logfile" &&
+#if $intype.infile == 'otulist' and $intype.groups:
+    mv intype_otu*.groups "$groupout"
+#else
+    mv intype_otu*.shared "$shared"
+#end if
     ]]></command>
     <inputs>
         <conditional name="intype">
@@ -67,6 +67,7 @@
                 <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -84,6 +85,7 @@
             <param name="infile" value="biom"/>
             <param name="otu" value="example.biom"/>
             <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with otu and group file-->
@@ -91,6 +93,7 @@
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label and group select-->
@@ -103,11 +106,11 @@
             <output_collection name="labelshares" count="3">
                 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -121,7 +124,7 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _rabund: https://www.mothur.org/wiki/Rabund_file
 .. _make.shared: https://www.mothur.org/wiki/Make.shared
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>