--- a/venn.xml	Tue Sep 05 17:08:23 2017 -0400
+++ b/venn.xml	Tue Mar 20 22:03:29 2018 -0400
@@ -7,35 +7,35 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$input.otu" input_otu.dat &&
+## create symlinks to input datasets
+ln -s '$input.otu' input_otu.dat &&
 
-        echo 'venn(
-            #if $input.source == "shared":
-                shared=input_otu.dat,
-                nseqs=$nseqs,
-                permute=$permute,
-                #if $input.groups:
-                    groups=${ str($input.groups).replace(",","-") },
-                #end if
-            #elif $input.source == "similarity":
-                list=input_otu.dat,
-                abund=$input.abund,
-            #end if
-            #if $input.label:
-                label=${ str($input.label).replace(",","-") },
-            #end if
-            #if $input.calc:
-                calc=${ str($input.calc).replace(",","-") },
-            #end if
-            fontsize=$fontsize,
-            sharedotus=$sharedotus
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'venn(
+    #if $input.source == "shared":
+        shared=input_otu.dat,
+        nseqs=$nseqs,
+        permute=$permute,
+        #if $input.groups:
+            groups=${ str($input.groups).replace(",","-") },
+        #end if
+    #elif $input.source == "similarity":
+        list=input_otu.dat,
+        abund=$input.abund,
+    #end if
+    #if $input.label:
+        label=${ str($input.label).replace(",","-") },
+    #end if
+    #if $input.calc:
+        calc=${ str($input.calc).replace(",","-") },
+    #end if
+    fontsize=$fontsize,
+    sharedotus=$sharedotus
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -82,6 +82,7 @@
         </param>
         <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
         <param name="sharedotus" type="boolean" falsevalue="false" truevalue="true" checked="true" label="sharedotus - This parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=T"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <collection name="sharedotus_out" type="list" label="${tool.name} on ${on_string}: sharedotus">
@@ -89,7 +90,7 @@
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sharedotus" format="tabular"/>
         </collection>
         <collection name="svgs_out" type="list" label="${tool.name} on ${on_string}: svg">
-            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.svg"/>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.svg" format="svg"/>
         </collection>
         <expand macro="logfile-output"/>
     </outputs>
@@ -100,11 +101,12 @@
             <param name="calc" value="sharedsobs,sharedchao"/>
             <param name="groups" value="forest,pasture"/>
             <output_collection name="sharedotus_out" count="35">
-                <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular"/>
+                <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular" />
             </output_collection>
             <output_collection name="svgs_out" count="72">
-                <element name="0.05.sharedsobs.forest-pasture" md5="b3c6eba426e2e2b9002699e5e62cb71d"/>
+                <element name="0.05.sharedsobs.forest-pasture" md5="e2dc0d5485520f5b22aa185ba91b123e" ftype="svg" />
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with list file -->
@@ -113,13 +115,13 @@
             <param name="calc" value="sobs,chao,ace"/>
             <param name="groups" value="forest,pasture"/>
             <output_collection name="svgs_out" count="108">
-                <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21"/>
+                <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21" ftype="svg"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -129,7 +131,6 @@
 
 .. _venn: https://www.mothur.org/wiki/Venn
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>