--- a/shhh.flows.xml	Tue Sep 05 16:49:40 2017 -0400
+++ b/shhh.flows.xml	Tue Mar 20 22:21:51 2018 -0400
@@ -7,28 +7,28 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s '$flow' flow.dat &&
-        ln -s '$prob.lookup' lookup.dat &&
+## create symlinks to input datasets
+ln -s '$flow' flow.dat &&
+ln -s '$prob.lookup' lookup.dat &&
 
-        ## Mothur can't handle scientific notation (i.e. 1e-6)
-        #set mindelta_decimal = "{:.12f}".format(float($mindelta))
-        echo 'shhh.flows(
-            flow=flow.dat,
-            lookup=lookup.dat,
-            maxiter=$maxiter,
-            mindelta=$mindelta_decimal,
-            cutoff=$cutoff,
-            sigma=$sigma,
-            order=$order,
-            large=$large,
-            processors='\${GALAXY_SLOTS:-8}'
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+## Mothur can't handle scientific notation (i.e. 1e-6)
+#set mindelta_decimal = "{:.12f}".format(float($mindelta))
+echo 'shhh.flows(
+    flow=flow.dat,
+    lookup=lookup.dat,
+    maxiter=$maxiter,
+    mindelta=$mindelta_decimal,
+    cutoff=$cutoff,
+    sigma=$sigma,
+    order=$order,
+    large=$large,
+    processors='\${GALAXY_SLOTS:-8}'
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file and usually trimmed by trim.flows"/>
@@ -52,6 +52,7 @@
         <param name="sigma" type="float" value="0.06" min="0.0" max="1.0" label="sigma - the dispersion of the data in the expectation-maximization step of the algorithm" help="default .06 (usually doesn't need to be changed)"/>
         <param name="large" type="integer" value="10000" min="1" label="large - split your flow file and process the pieces separately (default 10000)" help=""/>
         <param name="order" type="text" value="A" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -71,11 +72,11 @@
             <output name="shhh_names" md5="71c8fd857b547f237e4215306762ab3d" ftype="mothur.names"/>
             <output name="shhh_groups" md5="75a5293a71beeafe9f330e6f497ae350" ftype="mothur.groups"/>
             <output name="shhh_counts" md5="2257f2079668a0f992a14e4576063cf0" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -85,7 +86,6 @@
 
 .. _shhh.flows: https://www.mothur.org/wiki/Shhh.flows
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>