## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
    #if $annotate_source.ext == 'vcf_bgzip':
        ## File is bgzipped and tabixed already -> just symlink data and index
        #set $tabixed_file = 'tabixed.vcf.gz'
        ln -s '$annotate_source' $tabixed_file &&
        ln -s '$annotate_source.metadata.tabix_index' ${tabixed_file}.tbi &&
    #else:
        ## bgzip and index vcf or bed
        #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
        bgzip -c '$annotate_source' > '$tabixed_file' &&
        tabix -p '$annotate_source.ext' '$tabixed_file' &&
    #end if
    ## gemini annotate modifies its input database in-place so, in Galaxy,
    ## we need to create a copy first!
    cp '$infile' '$outfile' &&

    gemini annotate
        -f '$tabixed_file'
        -a $a.a_selector
        #if $a.a_selector == 'extract':
            #set $types = []
            #set $elements = []
            #set $column_names = []
            #set $operations = []
            #for $action in $a.actions:
                $types.append(str($action.column_type))
                $elements.append(str($action.element_to_extract).strip())
                $column_names.append(str($action.column_name).strip())
                $operations.append(str($action.operation))
            #end for

            -t #echo ",".join($types)
            -e '#echo ",".join($elements)#'
            -o #echo ",".join($operations)
            -c '#echo ",".join($column_names)#'
        #else:
            -c '${a.column_name}'
        #end if
        #if str($annotate_source.ext) != "bed":
            $region_only
        #end if
        '$outfile'