# HG changeset patch
# User iuc
# Date 1571214753 14400
# Node ID a15f2773a7d786eb30f32a2ceb911617fca5b6a1
# Parent  32da07a53d3b336026c3a26c3cd60dea28e14332
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"

diff -r 32da07a53d3b -r a15f2773a7d7 macros.xml
--- a/macros.xml	Tue Oct 08 08:24:28 2019 -0400
+++ b/macros.xml	Wed Oct 16 04:32:33 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 32da07a53d3b -r a15f2773a7d7 transit_hmm.xml
--- a/transit_hmm.xml	Tue Oct 08 08:24:28 2019 -0400
+++ b/transit_hmm.xml	Wed Oct 16 04:32:33 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_hmm" name="HMM" version="@VERSION@+galaxy1">
+<tool id="transit_hmm" name="HMM" version="@VERSION@+galaxy2">
     <description>- determine essentiality of a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -9,13 +9,12 @@
     	@LINK_INPUTS@
         transit hmm $input_files annotation.dat transit_out.txt
         @STANDARD_OPTIONS@
-        -r $replicates
         $loess
         ]]>
     </command>
     <inputs>
         <expand macro="standard_inputs">
-        	<expand macro="replicates" />
+        	<expand macro="handle_replicates" />
             <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
         </expand>
     </inputs>