--- a/create.database.xml	Tue Sep 05 16:49:27 2017 -0400
+++ b/create.database.xml	Tue Mar 20 21:54:19 2018 -0400
@@ -7,48 +7,52 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$repfasta" repfasta.dat &&
-        ln -s "$nameOrCount" nameOrCount.dat &&
-        ln -s "$constaxonomy" constaxonomy.dat &&
-        ln -s "$group" group.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$repfasta' repfasta.dat &&
+ln -s '$nameOrCount' nameOrCount.dat &&
+ln -s '$constaxonomy' constaxonomy.dat &&
+ln -s '$group' group.dat &&
 
-        echo 'create.database(
-            #if $otu.is_of_type("mothur.list"):
-                list=otu.dat
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat
-            #end if
-            ,repfasta=repfasta.dat
-            #if $nameOrCount.is_of_type("mothur.names"):
-                ,repname=nameOrCount.dat
-            #elif $nameOrCount.is_of_type("mothur.count_table"):
-                ,count=nameOrCount.dat
-            #end if
-            ,constaxonomy=constaxonomy.dat
-            #if $group:
-                ,group=group.dat
-            #end if
-            #if $label:
-                ,label=$label
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'create.database(
+    #if $otu.is_of_type("mothur.list"):
+        list=otu.dat
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat
+    #end if
+    ,repfasta=repfasta.dat
+    #if $nameOrCount.is_of_type("mothur.names"):
+        ,repname=nameOrCount.dat
+    #elif $nameOrCount.is_of_type("mothur.count_table"):
+        ,count=nameOrCount.dat
+    #end if
+    ,constaxonomy=constaxonomy.dat
+    #if $group:
+        ,group=group.dat
+    #end if
+    #if $label:
+        ,label=$label
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
-        <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
-        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/>
-        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/>
+        <param name="repfasta" type="data" format="fasta" optional="true" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
+        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="repname/count - Representative sequences"
+            help="rep.name file or rep.count_table file generated by get.oturep"/>
+        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy"
+            help="consensus taxonomy file output by classify.otu"/>
         <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
-        <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used">
+        <param name="label" type="select" label="label - OTU Labels" optional="true"
+            help="Select exactly one label. If none selected, first label in your list or shared file will be used">
             <expand macro="labeloptions"/>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -63,6 +67,7 @@
             <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
             <param name="label" value="unique"/>
             <output name="database" file="cd-test.database" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- Test with a mothur.count_table file -->
@@ -73,11 +78,11 @@
             <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
             <param name="label" value="unique"/>
             <output name="database" file="cd-test.database" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -91,7 +96,6 @@
 
 v.1.28.0: Updated to Mothur 1.33, added count paramter.
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>