--- a/sffinfo.xml	Tue Sep 05 17:14:44 2017 -0400
+++ b/sffinfo.xml	Tue Mar 20 22:19:08 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 "$sff" sff.dat &&
-        ln -s "$accnos" accnos.dat &&
-        #if $oligo.add == "yes":
-            ln -s "$oligo.oligos" oligo.oligos.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$sff' sff.dat &&
+ln -s '$accnos' accnos.dat &&
+#if $oligo.add == "yes":
+    ln -s '$oligo.oligos' oligo.oligos.dat &&
+#end if
 
-        echo 'sffinfo(
-            sff=sff.dat,
-            fasta=$fasta,
-            qfile=$qfile,
-            $sfftxt
-            flow=$flow,
-            trim=$trim
-            #if $accnos:
-                ,accnos=accnos.dat
-            #end if
-            #if $oligo.add == "yes":
-                ,oligos=oligo.oligos.dat
-                ,bdiffs=$oligo.bdiffs
-                ,pdiffs=$oligo.pdiffs
-                ,tdiffs=$oligo.tdiffs
-                ,ldiffs=$oligo.ldiffs
-                ,sdiffs=$oligo.sdiffs
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'sffinfo(
+    sff=sff.dat,
+    fasta=$fasta,
+    qfile=$qfile,
+    $sfftxt
+    flow=$flow,
+    trim=$trim
+    #if $accnos:
+        ,accnos=accnos.dat
+    #end if
+    #if $oligo.add == "yes":
+        ,oligos=oligo.oligos.dat
+        ,bdiffs=$oligo.bdiffs
+        ,pdiffs=$oligo.pdiffs
+        ,tdiffs=$oligo.tdiffs
+        ,ldiffs=$oligo.ldiffs
+        ,sdiffs=$oligo.sdiffs
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="sff" type="data" format="sff" label="sff - Sff data"/>
@@ -62,6 +62,7 @@
         <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
         <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
         <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -89,6 +90,7 @@
             <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
             <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
             <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with oligos file -->
@@ -98,12 +100,12 @@
             <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
             <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
             <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
-            <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/>
+            <output name="out_scrap" file="Fasting_Example1.scrap.sff" ftype="sff" compare="sim_size"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -113,7 +115,7 @@
 
 
 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>