--- a/shhh.flows.xml	Fri Jun 24 16:50:00 2016 -0400
+++ b/shhh.flows.xml	Thu May 18 18:22:58 2017 -0400
@@ -4,16 +4,20 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
-        ln -s "$flow" flow.dat &&
+        ln -s '$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($mindelta))
         echo 'shhh.flows(
             flow=flow.dat,
-            lookup=$prob.lookup,
+            lookup=lookup.dat,
             maxiter=$maxiter,
             mindelta=$mindelta_decimal,
             cutoff=$cutoff,
@@ -24,6 +28,7 @@
         )'
         | 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"/>
@@ -38,7 +43,7 @@
                 </param>
             </when>
             <when value="hist">
-                <param name="lookup" type="data" format="tabular" label="lookup - intensity value per homopolymer length" help="from http://www.mothur.org/wiki/Lookup_files"/>
+                <param name="lookup" type="data" format="tabular" label="lookup - intensity value per homopolymer length" help="from https://www.mothur.org/wiki/Lookup_files"/>
             </when>
         </conditional>
         <param name="maxiter" type="integer" value="1000" min="10" label="maxiter - maximum iterations to run (default 1000)" help="if the delta value does not first drop below the mindelta value. "/>
@@ -61,11 +66,11 @@
             <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/>
             <param name="source" value="hist"/>
             <param name="lookup" value="LookUp_Titanium.pat"/>
-            <output name="shhh_fasta" md5="dae330939c01e4831e2f804adc90493c" ftype="fasta"/>
-            <output name="shhh_qual" md5="47e8c7d953f276277d40375b2fb0feec" ftype="qual454"/>
-            <output name="shhh_names" md5="98326572926c744f4a1ea342ff7c7dcc" ftype="mothur.names"/>
-            <output name="shhh_groups" md5="e7f4237cef054ddf52a63ebad568a350" ftype="mothur.groups"/>
-            <output name="shhh_counts" md5="ae26201637dc3a64e6865c43c317a688" ftype="tabular"/>
+            <output name="shhh_fasta" md5="9e7ba8213d039ba2360648c79f6380da" ftype="fasta"/>
+            <output name="shhh_qual" md5="3ff0e8f575adc95ced285cc1704097ef" ftype="qual454"/>
+            <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"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
@@ -74,11 +79,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The shhh.flows_ command is Pat Schloss's translation of Chris Quince's PyroNoise algorithm [1] from C to C++ with the incorporation of mothur's bells and whistles. Based on processing of test datasets provided by Quince, shhh.flows gives the same/similar output to AmpliconNoise. shhh.flows uses a expectation-maximization algorithm to correct flowgrams to identify the idealized form of each flowgram and translate that flowgram to a DNA sequence. Our testing has shown that when Titanium data are trimmed to 450 flows using trim.flows, shhh.flows provides the highest quality data for any other method available. In contrast, when we use the min/max number of flows suggested by Quince of 360/720, the error rate is not that great. This much improved error rate does come at a computational cost. Whereas the features in trim.seqs take on the order of minutes, shhh.flows can take on the order of hours.  You will also need a lookup file that tells shhh.flows the probability of observing an intensity value for a given homopolymer length. You can get mothur-compatible files at: http://www.mothur.org/wiki/Lookup_files
+The shhh.flows_ command is Pat Schloss's translation of Chris Quince's PyroNoise algorithm [1] from C to C++ with the incorporation of mothur's bells and whistles. Based on processing of test datasets provided by Quince, shhh.flows gives the same/similar output to AmpliconNoise. shhh.flows uses a expectation-maximization algorithm to correct flowgrams to identify the idealized form of each flowgram and translate that flowgram to a DNA sequence. Our testing has shown that when Titanium data are trimmed to 450 flows using trim.flows, shhh.flows provides the highest quality data for any other method available. In contrast, when we use the min/max number of flows suggested by Quince of 360/720, the error rate is not that great. This much improved error rate does come at a computational cost. Whereas the features in trim.seqs take on the order of minutes, shhh.flows can take on the order of hours.  You will also need a lookup file that tells shhh.flows the probability of observing an intensity value for a given homopolymer length. You can get mothur-compatible files at: https://www.mothur.org/wiki/Lookup_files
 
-.. _shhh.flows: http://www.mothur.org/wiki/Shhh.flows
+.. _shhh.flows: https://www.mothur.org/wiki/Shhh.flows
 
 ]]>
     </help>