--- a/get.communitytype.xml	Tue Sep 05 17:11:06 2017 -0400
+++ b/get.communitytype.xml	Tue Mar 20 22:01:40 2018 -0400
@@ -7,37 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s '$otu' shared.dat &&
+## create symlinks to input datasets
+ln -s '$otu' shared.dat &&
 
-        echo 'get.communitytype(
-            shared=shared.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            method=$m.method,
-            #if $m.method == 'kmeans' or $m.method == 'pams':
-                calc=$m.calc,
-                iters=$m.iters,
-            #end if
-            #if int($subsample) == 0:
-                subsample=T,
-            #elif int($subsample) > 0:
-                subsample=$subsample,
-            #end if
-            minpartitions=$minpartitions,
-            maxpartitions=$maxpartitions,
-            optimizegap=$optimizegap,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.communitytype(
+    shared=shared.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    method=$m.method,
+    #if $m.method == 'kmeans' or $m.method == 'pams':
+        calc=$m.calc,
+        iters=$m.iters,
+    #end if
+    #if int($subsample) == 0:
+        subsample=T,
+    #elif int($subsample) > 0:
+        subsample=$subsample,
+    #end if
+    minpartitions=$minpartitions,
+    maxpartitions=$maxpartitions,
+    optimizegap=$optimizegap,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
@@ -77,6 +77,7 @@
         <param name="maxpartitions" type="integer" value="10" min="0" label="minpartitions" help=""/>
         <param name="optimizegap" type="integer" value="3" min="0" label="minpartitions" help=""/>
         <param name="subsample" type="integer" value="-1" min="-1" label="subsample" help="Ignored if negative, when set to 0 it uses the size of your smallest group (subsample=T)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -112,6 +113,7 @@
             <output_collection name="posterior" count="5">
                 <element name="1.dmm.1.mix" md5="fae04096d53d6980d8eb712e6ec8b0d2" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with all settings -->
@@ -141,6 +143,7 @@
             <output_collection name="posterior" count="4">
                 <element name="1.kmeans.1.mix" md5="43f4dfc2bcd1cf20db4f89ee90b6041c" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>