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Update SRMA wrapper to use data tables.

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This commit is contained in:
Daniel Blankenberg
2011-10-31 09:49:51 -04:00
parent 74c5e42ecd
commit 8b402babb2
2 changed files with 3 additions and 3 deletions
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tools/sr_mapping/srma_wrapper.py
+1 -1
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@@ -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' )
tools/sr_mapping/srma_wrapper.xml
+2 -2
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@@ -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}