details: http://www.bx.psu.edu/hg/galaxy/rev/d97f4e86be45 changeset: 2824:d97f4e86be45 user: Anton Nekrutenko anton@bx.psu.edu date: Fri Oct 02 11:02:14 2009 -0400 description: merge
0 file(s) affected in this change:
diffs (39 lines):
diff -r 2c0c81150dbd -r d97f4e86be45 tools/sr_mapping/bowtie_wrapper_code.py --- a/tools/sr_mapping/bowtie_wrapper_code.py Fri Oct 02 11:00:30 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper_code.py Fri Oct 02 11:02:14 2009 -0400 @@ -3,13 +3,14 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: refFile = param_dict['refGenomeSource']['indices'].value - dbkey = os.path.split(refFile)[1].split('.')[0] - # deal with the one odd case - if dbkey.find('chrM') >= 0: - dbkey = 'equCab2' - out_data['output'].set_dbkey(dbkey) except: try: refFile = param_dict['refGenomeSource']['ownFile'].dbkey except: - out_data['output'].set_dbkey('?') + out_data['output'].set_dbkey('?') + return + dbkey = os.path.split(refFile)[1].split('.')[0] + # deal with the one odd case + if dbkey.find('chrM') >= 0: + dbkey = 'equCab2' + out_data['output'].set_dbkey(dbkey) diff -r 2c0c81150dbd -r d97f4e86be45 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Oct 02 11:00:30 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Oct 02 11:02:14 2009 -0400 @@ -3,9 +3,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) except: try: refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey except: out_data['output'].set_dbkey('?') + return + out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0])