# HG changeset patch
# User iuc
# Date 1571214770 14400
# Node ID c68753eedf72406a4986ca09b4633ac88463c50f
# Parent  e4f44f327cf11a9a18d4c8ba638f59fa1cbc7925
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"

diff -r e4f44f327cf1 -r c68753eedf72 macros.xml
--- a/macros.xml	Tue Oct 08 08:24:46 2019 -0400
+++ b/macros.xml	Wed Oct 16 04:32:50 2019 -0400
@@ -18,10 +18,10 @@
         <yield />
         <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
     </xml>
-    <xml name="replicates">
-        <param name="replicates" type="select" label="How to handle replicates">
+    <xml name="handle_replicates">
+        <param name="handle_replicates" type="select" label="How to handle replicates" value="Mean">
+        	<option value="Sum">Sum</option>
         	<option value="Mean">Mean</option>
-        	<option value="Sum">Sum</option>
         </param>
     </xml>
     <xml name="inputs">
@@ -78,5 +78,6 @@
         -iN $nterm
         -tC $cterm
         -n $normalization
+        -r $handle_replicates
     </token>
 </macros>
diff -r e4f44f327cf1 -r c68753eedf72 transit_tn5gaps.xml
--- a/transit_tn5gaps.xml	Tue Oct 08 08:24:46 2019 -0400
+++ b/transit_tn5gaps.xml	Wed Oct 16 04:32:50 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 :