Mercurial > repos > devteam > cuffmerge

comparison cuffmerge_wrapper.py @ 13:cf747d1bd79a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:12:38 -0500
parents 1707a530e598
children
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12:1707a530e598 13:cf747d1bd79a
26 # Outputs. 26 # Outputs.
27 parser.add_option('', '--merged-transcripts', dest='merged_transcripts') 27 parser.add_option('', '--merged-transcripts', dest='merged_transcripts')
28 parser.add_option('--min-isoform-fraction', dest='min_isoform_fraction') 28 parser.add_option('--min-isoform-fraction', dest='min_isoform_fraction')
29 29
30 (options, args) = parser.parse_args() 30 (options, args) = parser.parse_args()
31
32 # output version # of tool
33 try:
34 with tempfile.NamedTemporaryFile() as tmp_stdout:
35 returncode = subprocess.call(args='cuffmerge -v 2>&1', stdout=tmp_stdout, shell=True)
36 stdout = None
37 with open(tmp_stdout.name) as tmp_stdout2:
38 for line in tmp_stdout2:
39 if line.lower().find('merge_cuff_asms v') >= 0:
40 stdout = line.strip()
41 break
42 if stdout:
43 sys.stdout.write('%s\n' % stdout)
44 else:
45 raise Exception
46 except:
47 sys.stdout.write('Could not determine Cuffmerge version\n')
48 31
49 # Set/link to sequence file. 32 # Set/link to sequence file.
50 if options.use_seq_data: 33 if options.use_seq_data:
51 if options.ref_file: 34 if options.ref_file:
52 # Sequence data from history. 35 # Sequence data from history.