# HG changeset patch
# User bgruening
# Date 1551224504 18000
# Node ID b26a0df246fd1eb1505dfdafea14c220044d2526
# Parent  cbfd9b10eff6906276ff9164e044a8e2c0a68c85
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b

diff -r cbfd9b10eff6 -r b26a0df246fd bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml	Fri Feb 22 14:15:24 2019 -0500
+++ b/bismark_bowtie2_wrapper.xml	Tue Feb 26 18:41:44 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.1" profile="18.01">
+<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.2" profile="18.01">
     <description>Bisulfite reads mapper</description>
     <requirements>
         <requirement type="package" version="0.20.0">bismark</requirement>
@@ -252,7 +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"
+                <param argument="--non-directional" name="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 -->
diff -r cbfd9b10eff6 -r b26a0df246fd bismark_wrapper.py
--- a/bismark_wrapper.py	Fri Feb 22 14:15:24 2019 -0500
+++ b/bismark_wrapper.py	Tue Feb 26 18:41:44 2019 -0500
@@ -68,6 +68,7 @@
     parser.add_argument('--fastq', action='store_true', help='Query filetype is in FASTQ format')
     parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format')
     parser.add_argument('--phred64-quals', dest='phred64', action="store_true")
+    parser.add_argument('--non-directional', dest='non_directional', action="store_true")
 
     parser.add_argument('--skip-reads', dest='skip_reads', type=int)
     parser.add_argument('--qupto', type=int)
@@ -184,6 +185,8 @@
         cmd.extend(['--upto', 'args.qupto'])
     if args.phred64:
         cmd.append('--phred64-quals')
+    if args.non_directional:
+       cmd.append('--non-directional')
     if args.suppress_header:
         cmd.append('--sam-no-hd')
     if args.output_unmapped_reads or (args.output_unmapped_reads_l and args.output_unmapped_reads_r):