From 8b402babb2821985a4aee6ff2163ee1817357ac3 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 31 Oct 2011 09:49:51 -0400 Subject: [PATCH] Update SRMA wrapper to use data tables. --- tools/sr_mapping/srma_wrapper.py | 2 +- tools/sr_mapping/srma_wrapper.xml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/sr_mapping/srma_wrapper.py b/tools/sr_mapping/srma_wrapper.py index 1c6c3f6e90c..5646756aded 100644 --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -29,7 +29,7 @@ def __main__(): 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 --git a/tools/sr_mapping/srma_wrapper.xml b/tools/sr_mapping/srma_wrapper.xml index ec12a258411..ccb8ab290bc 100644 --- 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}