--- a/transit_tn5gaps.xml	Tue Oct 08 08:22:57 2019 -0400
+++ b/transit_tn5gaps.xml	Wed Oct 16 04:30:48 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy1">
+<tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy2">
     <description>- determine essential genes</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,7 @@
     </command>
     <inputs>
         <expand macro="standard_inputs">
+            <expand macro="handle_replicates" />
             <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" />
         </expand>
     </inputs>
@@ -59,11 +60,12 @@
 
 Optional Arguments:
        -m <integer>    :=  Smallest read-count to consider. Default: -m 1
-       -r <string>     :=  How to handle replicates. Sum or Mean. Default: -r Sum
+       -r <string>     :=  How to handle replicates. Sum or Mean. Default: -r Mean
        --iN <float>     :=  Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0
        --iC <float>     :=  Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0
        -n <string>      := Determines which normalization method to use. Default -n TTR
 
+
 - Minimum Read: The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be susceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1.
 - Replicates: Determines how to deal with replicates by averaging the read-counts or summing read counts across datasets. This should not have an affect for the Gumbel method, aside from potentially affecting spurious reads.
 - Normalisation :