1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/34ccc65185b3/ changeset: 34ccc65185b3 user: dan date: 2011-10-31 14:49:51 summary: Update SRMA wrapper to use data tables. affected #: 2 files diff -r 520773ea8c879c2ff3705118fa0913673e1c70c6 -r 34ccc65185b34cb68f543fe041f3396e7897757c tools/sr_mapping/srma_wrapper.py --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -29,7 +29,7 @@ parser = optparse.OptionParser() parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' ) parser.add_option( '-u', '--refUID', dest='refUID', help='The pre-index reference genome unique Identifier' ) - parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' ) + #parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' ) parser.add_option( '-i', '--input', dest='input', help='The SAM/BAM input file' ) parser.add_option( '-I', '--inputIndex', dest='inputIndex', help='The SAM/BAM input index file' ) parser.add_option( '-o', '--output', dest='output', help='The SAM/BAM output file' ) diff -r 520773ea8c879c2ff3705118fa0913673e1c70c6 -r 34ccc65185b34cb68f543fe041f3396e7897757c tools/sr_mapping/srma_wrapper.xml --- a/tools/sr_mapping/srma_wrapper.xml +++ b/tools/sr_mapping/srma_wrapper.xml @@ -4,9 +4,9 @@ #if $refGenomeSource.refGenomeSource_type == "history": --ref=$refGenomeSource.ownFile #else: - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.ref.fields.path}" --refUID=$refGenomeSource.ref - --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc + ##--refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc #end if --input=$input --inputIndex=${input.metadata.bam_index} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.