Mercurial > repos > bgruening > bismark
changeset 10:7bffcb6fc81d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b
| author | bgruening |
|---|---|
| date | Tue, 26 Feb 2019 18:42:28 -0500 |
| parents | 1a88b0f2669f |
| children | 1f15ad5ca867 |
| files | bismark_bowtie2_wrapper.xml bismark_wrapper.py |
| diffstat | 2 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/bismark_bowtie2_wrapper.xml Fri Feb 22 14:15:46 2019 -0500 +++ b/bismark_bowtie2_wrapper.xml Tue Feb 26 18:42:28 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 -->
--- a/bismark_wrapper.py Fri Feb 22 14:15:46 2019 -0500 +++ b/bismark_wrapper.py Tue Feb 26 18:42:28 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):