# HG changeset patch
# User bgruening
# Date 1550862946 18000
# Node ID 1a88b0f2669f84845a5c49d15e8174b9c8626e5c
# Parent  9bfe38410155e6fe2416063951abf4f4c4bdd50c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 5da44021266ae8cd3cdffc045ae53490e2a59a05

diff -r 9bfe38410155 -r 1a88b0f2669f bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Wed Aug 22 08:09:42 2018 -0400
+++ b/bismark_bowtie2_wrapper.xml	Fri Feb 22 14:15:46 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.1" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.20.0">bismark</requirement>
@@ -102,6 +102,8 @@
             ## if set, disable the original behaviour
             $params.no_discordant
 
+            $params.non_directional
+
             #if $params.bismark_stdout:
                 --stdout '$output_stdout'
             #end if
@@ -250,6 +252,8 @@
                        label="Write the bismark output and summary information to an extra file"/>
                 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
                        label="Offer all report files concatenated in one file (Mapping Report)"/>
+                <param argument="--non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="false"
+                       label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
 
                 <!--end output options -->
             </when>  <!-- full -->