--- a/hyphy_sm19.xml	Fri Mar 27 13:17:03 2020 -0400
+++ b/hyphy_sm19.xml	Wed Apr 22 12:10:17 2020 -0400
@@ -13,6 +13,7 @@
             '${partition.regex}'
         #end for
         $replicates
+        --output '$sm19_output'
         ]]></command>
     <inputs>
         <param name="input_file" type="data" format="nhx" label="Input tree"/>
@@ -32,7 +33,7 @@
         <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
     </inputs>
     <outputs>
-        <data name="sm19_output" format="hyphy_results.json" from_work_dir="sm19_input.nhx.json"/>
+        <data name="sm19_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
@@ -66,11 +67,11 @@
 
 SM2019 : Structured Slatkin-Maddison
 ====================================
-    
+
 What does this do?
 ------------------
 
-Test for evidence of genetically segregated populations, using a "detuned" version of 
+Test for evidence of genetically segregated populations, using a "detuned" version of
 the Slatkin-Maddison test.
 
 Brief description
@@ -108,8 +109,8 @@
     06,x_US_x_A_13C:-4.34574e-06):4.34574e-06,((x_US_x_A_08C:0.0029538,
     x_US_x_A_09C:-1.31511e-05):0.00296627,x_US_x_A_10C:-8.69148e-06):4.
     34574e-06,x_US_x_A_15C:-4.34574e-06);
-    
-Which can be partitioned into two groups of leaves, those that end in "P", and those that 
+
+Which can be partitioned into two groups of leaves, those that end in "P", and those that
 end in "C"
 
 1. Reg-exp 1: `P^`