#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 lineage_wf
    'bins'
    'output'
    $tree_analyze.reduced_tree
    $tree_analyze.ali
    $tree_analyze.nt
    $tree_analyze.genes
    --unique '$lineage_set.unique'
    --multi '$lineage_set.multi'
    $lineage_set.force_domain
    $lineage_set.no_refinement
    $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}
    --pplacer_threads \${GALAXY_SLOTS:-1}