comparison cuffcompare_wrapper.py @ 9:e66b9b5b8580 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

8:1322b73ffe44

    # Outputs.
    parser.add_option('', '--combined-transcripts', dest='combined_transcripts')

    (options, args) = parser.parse_args()

    # output version # of tool
    try:
        with tempfile.NamedTemporaryFile() as tmp_stdout:
            returncode = subprocess.call(args='cuffcompare 2>&1', stdout=tmp_stdout, shell=True)
            stdout = None
            with open(tmp_stdout.name) as tmp_stdout2:
                for line in tmp_stdout2:
                    if line.lower().find('cuffcompare v') >= 0:
                        stdout = line.strip()
                        break
        if stdout:
            sys.stdout.write('%s\n' % stdout)
        else:
            raise Exception
    except:
        sys.stdout.write('Could not determine Cuffcompare version\n')

    # Set/link to sequence file.
    if options.use_seq_data:
        if options.ref_file:
            # Sequence data from history.

9:e66b9b5b8580

    # Outputs.
    parser.add_option('', '--combined-transcripts', dest='combined_transcripts')

    (options, args) = parser.parse_args()

    # Set/link to sequence file.
    if options.use_seq_data:
        if options.ref_file:
            # Sequence data from history.