--- a/make.biom.xml	Fri Sep 08 14:47:45 2017 -0400
+++ b/make.biom.xml	Tue Mar 20 22:18:35 2018 -0400
@@ -7,45 +7,45 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$constaxonomy" constaxonomy.dat &&
-        ln -s "$metadata" metadata.dat &&
-        #if $picrustc.use == "yes":
-            ln -s "$picrustc.picrust" picrustc.picrust.dat &&
-            ln -s "$picrustc.reftax" picrustc.reftax.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$constaxonomy' constaxonomy.dat &&
+ln -s '$metadata' metadata.dat &&
+#if $picrustc.use == "yes":
+    ln -s '$picrustc.picrust' picrustc.picrust.dat &&
+    ln -s '$picrustc.reftax' picrustc.reftax.dat &&
+#end if
 
-        echo 'make.biom(
-            shared=otu.dat,
-            #if $constaxonomy:
-                constaxonomy=constaxonomy.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            #if $metadata:
-                metadata=metadata.dat,
-            #end if
-            #if $picrustc.use == "yes":
-                picrust=picrustc.picrust.dat,
-                reftaxonomy=picrustc.reftax.dat,
-            #end if
-            matrixtype=$matrixtype
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'make.biom(
+    shared=otu.dat,
+    #if $constaxonomy:
+        constaxonomy=constaxonomy.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    #if $metadata:
+        metadata=metadata.dat,
+    #end if
+    #if $picrustc.use == "yes":
+        picrust=picrustc.picrust.dat,
+        reftaxonomy=picrustc.reftax.dat,
+    #end if
+    matrixtype=$matrixtype
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
         <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
-        <param name="metadata" type="data" format="tabular" label="metadata" optional="true" help="You can add sample data support here"/>
+        <param name="metadata" type="data" format="tabular,txt" label="metadata" optional="true" help="You can add sample data support here"/>
         <conditional name="picrustc">
             <param name="use" type="select" label="use picrust program">
                 <option value="no" selected="true">no</option>
@@ -69,10 +69,11 @@
         <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made">
             <expand macro="labeloptions"/>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: calculators">
+        <collection name="biomfiles" type="list" label="${tool.name} on ${on_string}: biom files">
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.biom" format="biom1"/>
         </collection>
     </outputs>
@@ -89,6 +90,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with subset of labels and groups-->
@@ -105,6 +107,7 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with constaxonomy and metadata -->
@@ -120,12 +123,12 @@
                     </assert_contents>
                 </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <!-- TODO: test with picrust option (need file with greengenes OTU IDs) -->
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -138,7 +141,7 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _biom:  http://biom-format.org/documentation/biom_format.html
 .. _make.biom: https://www.mothur.org/wiki/Make.biom
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>