I found two mistakes in the code of the bwa wrapper .

The first one comes from the following error message:

  File "/galaxy-dist/tools/bwa_wrappers/bwa_wrapper.py", line 79
parser.add_option( '-y', '--ion', dest='ion', action="store_true, help='Ion Torrent data mode using bwasw' )
SyntaxError: EOL while scanning string literal

in the bwa_wrapper.py file line 79:
-there is a missing double quote character after sur store_true

in the bwasw_wrapper.xml file line 9:
-there --ion option must not have a value

Till, with those corrections, the mapping with bwa for Ion Torrent does not seem to work properly. My ouput sam file had only the header in it.

Best regards



Dr. Yec'han LAIZET
Ingenieur Bioinformatique
Tel: +33 (0)5 57 12 27 75
Plateforme Genome Transcriptome
Equipe Genetique
69 route d'Arcachon
33612 CESTAS

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