#import re

#if $blast_input.is_of_type('daa'):
    #set blast_format = 'DAA'
#else if $blast_input.is_of_type('txt'):
    #set blast_format = 'BlastText'
#else if $blast_input.is_of_type('blastxml'):
    #set blast_format = 'BlastXML'
#else if $blast_input.is_of_type('tabular'):
    #set blast_format = 'BlastTab'
#else if $blast_input.is_of_type('sam'):
    #set blast_format = 'SAM'
#end if
#set blast_ext = '.' + $blast_format
#if $blast_input.ext.endswith('.gz'):
    #set blast_ext = $blast_ext + '.gz'
#end if

#set blast_input_identifier = 'blast_input' + $blast_ext
ln -s '${blast_input}' '${blast_input_identifier}' &&

blast2lca 
    --input '${blast_input_identifier}'
    --format '${blast_format}'
    --mode '${mode}'
    $advanced_options.showRanks
    $advanced_options.officialRanksOnly
    $advanced_options.showTaxIds
    --minScore $advanced_options.minScore
    --maxExpected $advanced_options.maxExpected
    --topPercent $advanced_options.topPercent
    --minPercentIdentity $advanced_options.minPercentIdentity
    --maxKeggPerRead $advanced_options.maxKeggPerRead
    $advanced_options.applyTopPercentKegg
    $advanced_options.parseTaxonNames
    #if $advanced_options.mapDB:
        --mapDB '$advanced_options.mapDB'
    #end if
    #if $advanced_options.acc2taxa:
        --acc2taxa '$advanced_options.acc2taxa'
    #end if
    #if $advanced_options.syn2taxa:
        --syn2taxa '$advanced_options.syn2taxa'
    #end if
    #if $advanced_options.acc2kegg:
        --acc2kegg '$advanced_options.acc2kegg'
    #end if
    #if $advanced_options.syn2kegg:
        --syn2kegg '$advanced_options.syn2kegg'
    #end if
    $advanced_options.firstWordIsAccession
    #if str($advanced_options.accessionTags) != '':
        --accessionTags '$advanced_options.maccessionTags'
    #end if
    #if $advanced_options.kegg:
        --kegg
        --keggOutput '$kegg_output'
    #end if
    --output '${taxonomy_output}'