#import re
mkdir 'bins' &&
#if $bins.select == 'collection'
    #for $b in $bins.bins_coll
        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
    #end for
#else
    #for $b in $bins.bins_ind
        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
    #end for
#end if


checkm taxonomy_wf
    '$rank_taxon.rank'
    '$rank_taxon.taxon'
    'bins'
    'output'
    $analyze.ali
    $analyze.nt
    $analyze.genes
    $qa.individual_markers
    $qa.skip_adj_correction
    $qa.skip_pseudogene_correction
    --aai_strain $qa.aai_strain
    $qa.ignore_thresholds
    --e_value $qa.e_value
    --length $qa.length
    --file '$results'
    --tab_table
    --extension 'fasta'
    --threads \${GALAXY_SLOTS:-1}