changeset 3:0e0618c96ca4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"

--- a/macros.xml	Tue Oct 08 08:23:54 2019 -0400
+++ b/macros.xml	Wed Oct 16 04:31:43 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>

--- a/transit_resampling.xml	Tue Oct 08 08:23:54 2019 -0400
+++ b/transit_resampling.xml	Wed Oct 16 04:31:43 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1">
+<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy2">
     <description>- determine per-gene p-values</description>
     <macros>
         <import>macros.xml</import>
@@ -18,6 +18,7 @@
     </command>
     <inputs>
         <expand macro="standard_inputs">
+            <expand macro="handle_replicates" />
             <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
             <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
             <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
@@ -86,6 +87,7 @@
 -ez             :=  Exclude rows with zero accross conditions. Default: Off
 --pc            :=  Pseudocounts to be added at each site. Default: 0
 -l              :=  Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
+-r <string>     :=  How to handle replicates. Sum, Mean. Default: -r Mean
 --iN <float>     :=  Ignore TAs occuring at given fraction of the N terminus. Default: 0.0
 --iC <float>     :=  Ignore TAs occuring at given fraction of the C terminus. Default: 0.0
 --ctrl_lib      :=  String of letters representing library of control files in order e.g. 'AABB' Default: empty. Letters used must also be used in --exp_lib. If non-empty, resampling will limit permutations to within-libraries.