diff macros.xml @ 2:c980be2c002c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada"
author iuc
date Tue, 08 Oct 2019 08:24:12 -0400
parents 202a99525669
children ecce0cbe659f
line wrap: on
line diff
--- a/macros.xml	Tue Jun 25 17:43:58 2019 -0400
+++ b/macros.xml	Tue Oct 08 08:24:12 2019 -0400
@@ -9,10 +9,11 @@
 	<xml name="requirements">
 		<requirements>
 			<requirement type="package" version="@VERSION@">transit</requirement>
+            <requirement type="package" version="3.7">python</requirement>
 			<yield />
 		</requirements>
 	</xml>
-	<token name="@VERSION@">2.5.2</token>
+	<token name="@VERSION@">3.0.1</token>
 	<xml name="outputs">
         <yield />
         <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" />
@@ -43,10 +44,22 @@
         <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." />
         <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." />
     </xml>
+    <xml name="normal">
+        <param name="normalization" argument="-n" type="select" label="Normalization method"  value="TTR">
+            <option value="TTR">TTR</option>
+            <option value="nonorm">No Normalization</option>
+            <option value="nzmean">Non-Zero Mean</option>
+            <option value="totreads">Total read counts</option>
+            <option value="zinfnb">Zero inflated Negative Binomial model</option>
+            <option value="quantile">Quantile Normalization</option>
+            <option value="betageom">Beta-Geometric Correction</option>
+        </param>
+    </xml>
     <xml name="standard_inputs">
     	<expand macro="inputs" />
     	<yield />
     	<expand macro="ignore_tas" />
+    	<expand macro="normal" />
     </xml>
     <token name="@LINK_INPUTS@">
         <![CDATA[
@@ -64,5 +77,6 @@
     <token name="@STANDARD_OPTIONS@">
         -iN $nterm
         -tC $cterm
+        -n $normalization
     </token>
 </macros>