details: http://www.bx.psu.edu/hg/galaxy/rev/e71a3d03a529 changeset: 3725:e71a3d03a529 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Fri Apr 30 15:45:32 2010 -0400 description: Fix dbkey setting for BWA. diffstat: tools/sr_mapping/bwa_wrapper_code.py | 9 ++++----- 1 files changed, 4 insertions(+), 5 deletions(-) diffs (19 lines): diff -r 007f175c8b88 -r e71a3d03a529 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:27:41 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:45:32 2010 -0400 @@ -2,11 +2,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + refFile = param_dict[ 'genomeSource' ][ 'indices' ].value except: try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + refFile = param_dict[ 'genomeSource' ][ 'ownFile' ].dbkey except: - out_data['output'].set_dbkey('?') - return - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + refFile = '?' + out_data[ 'output' ].set_dbkey( os.path.split( refFile )[1].split( '.' )[0] )