--- a/remove.rare.xml	Fri Sep 08 14:35:56 2017 -0400
+++ b/remove.rare.xml	Tue Mar 20 21:57:22 2018 -0400
@@ -7,46 +7,46 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.otu" input_otu.dat &&
-        #if $input.source == 'list':
-            ln -s "$input.group" input.group.dat &&
-            ln -s "$input.count" input.count.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$input.otu' input_otu.dat &&
+#if $input.source == 'list':
+    ln -s '$input.group' input.group.dat &&
+    ln -s '$input.count' input.count.dat &&
+#end if
 
-        echo 'remove.rare(
-            #if $input.otu.is_of_type("mothur.rabund"):
-                rabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.sabund"):
-                sabund=input_otu.dat,
-            #elif $input.otu.is_of_type("mothur.list"):
-                list=input_otu.dat,
-                #if $input.group:
-                    group=input.group.dat,
-                #end if
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-                #if $input.count:
-                    count=input.count.dat,
-                #end if
-            #elif $input.otu.is_of_type("mothur.shared"):
-                shared=input_otu.dat,
-                bygroup=$input.bygroup,
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-            #end if
-            #if $input.label:
-                label=${ str($input.label).replace(",","-") },
-            #end if
-            nseqs=$nseqs
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'remove.rare(
+    #if $input.otu.is_of_type("mothur.rabund"):
+        rabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.sabund"):
+        sabund=input_otu.dat,
+    #elif $input.otu.is_of_type("mothur.list"):
+        list=input_otu.dat,
+        #if $input.group:
+            group=input.group.dat,
+        #end if
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+        #if $input.count:
+            count=input.count.dat,
+        #end if
+    #elif $input.otu.is_of_type("mothur.shared"):
+        shared=input_otu.dat,
+        bygroup=$input.bygroup,
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+    #end if
+    #if $input.label:
+        label=${ str($input.label).replace(",","-") },
+    #end if
+    nseqs=$nseqs
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -88,6 +88,7 @@
             </when>
         </conditional>
         <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -107,6 +108,7 @@
             <param name="source" value="list"/>
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list and group file -->
@@ -116,6 +118,7 @@
             <param name="groups" value="forest,pasture"/>
             <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
             <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared file -->
@@ -124,6 +127,7 @@
             <output_collection name="pick_shared" count="36">
                 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared file and label/group select -->
@@ -135,17 +139,18 @@
             <output_collection name="pick_shared" count="3">
                 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with rabund/sabund file -->
             <param name="source" value="default"/>
             <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
             <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -159,7 +164,6 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>