The key lines in the wrapper are: -- <options from_data_table="tophat_indexes"> <filter type="sort_by" column="2"/> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> -- This code refers to the tool_data_table_conf.xml file, where tophat_indexes is defined: -- <!-- Locations of indexes in the Bowtie mapper format for TopHat to use --> <table name="tophat_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices.loc" /> </table> -- So you can see that Tophat uses the tool-data/bowtie_indices.loc file, which is reasonable because these tools share the same index format. Best, J. On Jul 23, 2012, at 5:25 PM, Andre Gatorano wrote:

Which .loc file corresponds to tophat? I looked through the .xml file for the wrapper and it made no reference to any .loc file.

-- Andre Gatorano 847-845-9284 University of California San Diego

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