--- a/summary.single.xml	Tue Sep 05 16:54:08 2017 -0400
+++ b/summary.single.xml	Tue Mar 20 22:00:33 2018 -0400
@@ -7,51 +7,51 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'summary.single(
-            #if $otu.is_of_type("mothur.rabund"):
-                rabund=otu.dat
-            #elif $otu.is_of_type("mothur.sabund"):
-                sabund=otu.dat
-            #elif $otu.is_of_type("mothur.list"):
-                list=otu.dat
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat,
-                groupmode=$groupmode
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $calc:
-                ,calc=${ str($calc).replace(",","-") }
-            #end if
-            #if $abund:
-                ,abund=$abund
-            #end if
-            #if $size:
-                ,size=$size
-            #end if
-            #if $subsample.use == 'yes':
-                #if $subsample.subsample:
-                    ,subsample=$subsample.subsample
-                #else
-                    ,subsample=T
-                #end if
-                #if $subsample.iters:
-                    ,iters=$subsample.iters
-                #end if
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
-            && mv otu.*ave-std.summary otu.ave-std
+echo 'summary.single(
+    #if $otu.is_of_type("mothur.rabund"):
+        rabund=otu.dat
+    #elif $otu.is_of_type("mothur.sabund"):
+        sabund=otu.dat
+    #elif $otu.is_of_type("mothur.list"):
+        list=otu.dat
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat,
+        groupmode=$groupmode
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    #if $calc:
+        ,calc=${ str($calc).replace(",","-") }
+    #end if
+    #if $abund:
+        ,abund=$abund
+    #end if
+    #if $size:
+        ,size=$size
+    #end if
+    #if $subsample.use == 'yes':
+        #if $subsample.subsample:
+            ,subsample=$subsample.subsample
+        #else
+            ,subsample=T
         #end if
+        #if $subsample.iters:
+            ,iters=$subsample.iters
+        #end if
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+#if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
+    && mv otu.*ave_std.summary otu.ave-std
+#end if
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
@@ -99,6 +99,7 @@
             <when value="no"/>
         </conditional>
         <param name="groupmode" type="boolean" truevalue="true" falsevalue="false" checked="true" label="groupmode - Collate shared summary results in one file" help="If false, create a summary file per group."/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -117,6 +118,7 @@
         <test><!-- test with shared and default params -->
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output name="summary" md5="eaf5304b383c3c5764193ac7f49589db" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label select and all calculators -->
@@ -124,6 +126,7 @@
             <param name="label" value="0.05,0.22,0.32"/>
             <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
             <output name="summary" md5="06039951e867e7d397db08aeb668f94f" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared and not groupmode -->
@@ -132,6 +135,7 @@
             <output_collection name="summaryfiles" count="2">
                 <element name="forest" md5="96e2c1213f25d6c342ba87ab3d2de6bf" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with rabund and subsample -->
@@ -153,11 +157,11 @@
                     <has_text text="0.05"/>
                 </assert_contents>
             </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -167,7 +171,7 @@
 
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _summary.single: https://www.mothur.org/wiki/Summary.single
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>