Mercurial > repos > bgruening > bismark
diff bismark_wrapper.py @ 17:aa9bf0f29a9f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit d85012b50faac3234496bb51e2a29c2d8c113bde"
author | bgruening |
---|---|
date | Wed, 28 Aug 2019 07:08:45 -0400 |
parents | a4504327c890 |
children | bb74e17e47d7 |
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--- a/bismark_wrapper.py Wed Aug 21 12:59:48 2019 -0400 +++ b/bismark_wrapper.py Wed Aug 28 07:08:45 2019 -0400 @@ -69,6 +69,7 @@ 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('--pbat', dest='pbat', action="store_true") parser.add_argument('--skip-reads', dest='skip_reads', type=int) parser.add_argument('--score-min', dest='score_min', type=str) @@ -153,7 +154,9 @@ # Build bismark command tmp_bismark_dir = tempfile.mkdtemp() output_dir = os.path.join(tmp_bismark_dir, 'results') - cmd = ['bismark', '--bam', '--gzip', '--temp_dir', tmp_bismark_dir, '-o', output_dir, '--quiet'] + cmd = ['bismark', '--bam', '--temp_dir', tmp_bismark_dir, '-o', output_dir, '--quiet'] + if not args.pbat: + cmd.append('--gzip') if args.fasta: # the query input files (specified as mate1,mate2 or singles) are FastA @@ -187,6 +190,8 @@ cmd.append('--phred64-quals') if args.non_directional: cmd.append('--non-directional') + if args.pbat: + cmd.append('--pbat') 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): @@ -223,24 +228,24 @@ output_report_file.close() if args.output_suppressed_reads: - if glob(os.path.join(output_dir, '*ambiguous_reads.txt')): - shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads.txt'))[0], args.output_suppressed_reads) + if glob(os.path.join(output_dir, '*ambiguous_reads.*')): + shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads.*'))[0], args.output_suppressed_reads) if args.output_suppressed_reads_l: - if glob(os.path.join(output_dir, '*ambiguous_reads_1.txt')): - shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_1.txt'))[0], args.output_suppressed_reads_l) + if glob(os.path.join(output_dir, '*ambiguous_reads_1.*')): + shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_1.*'))[0], args.output_suppressed_reads_l) if args.output_suppressed_reads_r: - if glob(os.path.join(output_dir, '*ambiguous_reads_2.txt')): - shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_2.txt'))[0], args.output_suppressed_reads_r) + if glob(os.path.join(output_dir, '*ambiguous_reads_2.*')): + shutil.move(glob(os.path.join(output_dir, '*ambiguous_reads_2.*'))[0], args.output_suppressed_reads_r) if args.output_unmapped_reads: - if glob(os.path.join(output_dir, '*unmapped_reads.txt')): - shutil.move(glob(os.path.join(output_dir, '*unmapped_reads.txt'))[0], args.output_unmapped_reads) + if glob(os.path.join(output_dir, '*unmapped_reads.*')): + shutil.move(glob(os.path.join(output_dir, '*unmapped_reads.*'))[0], args.output_unmapped_reads) if args.output_unmapped_reads_l: - if glob(os.path.join(output_dir, '*unmapped_reads_1.txt')): - shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_1.txt'))[0], args.output_unmapped_reads_l) + if glob(os.path.join(output_dir, '*unmapped_reads_1.*')): + shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_1.*'))[0], args.output_unmapped_reads_l) if args.output_unmapped_reads_r: - if glob(os.path.join(output_dir, '*unmapped_reads_2.txt')): - shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_2.txt'))[0], args.output_unmapped_reads_r) + if glob(os.path.join(output_dir, '*unmapped_reads_2.*')): + shutil.move(glob(os.path.join(output_dir, '*unmapped_reads_2.*'))[0], args.output_unmapped_reads_r) try: # merge all bam files