#import re
    #import os.path
    
    #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta')
    ln -s '$input' '$named_input' &&
    

    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile '${named_input}'

    #if $adv_param.unicycler_contigs:
      --unicycler_contigs 
    #end if   

    #if $adv_param.run_overhang:
      --run_overhang
    #end if 
    
    #if $adv_param.debug:
      --debug
    #end if

    #if $adv_param.plasmid_db
      --plasmid_db '$adv_param.plasmid_db'
    #end if

    #if $adv_param.plasmid_mash_db
      --plasmid_mash_db '$adv_param.plasmid_mash_db'
    #end if

    #if $adv_param.plasmid_meta
      --plasmid_meta '$adv_param.plasmid_meta'
    #end if

    #if $adv_param.repetitive_mask
      --repetitive_mask '$adv_param.repetitive_mask'
    #end if

   #if $adv_param.plasmid_mob
   --plasmid_mob '$adv_param.plasmid_mob'
   #end if
   
   #if $adv_param.plasmid_mpf
   --plasmid_mpf '$adv_param.plasmid_mpf'
   #end if

   #if $adv_param.plasmid_orit
   --plasmid_orit '$adv_param.plasmid_orit'
   #end if

   #if $adv_param.filter_db
   --filter_db '$adv_param.filter_db'
   #end if

    --mash_genome_neighbor_threshold '${adv_param.mash_genome_neighbor_threshold}'
    --primary_cluster_dist '${adv_param.primary_cluster_dist}'
    --secondary_cluster_dist '${adv_param.secondary_cluster_dist}'
    --max_contig_size '${adv_param.max_contig_size}'
    --max_plasmid_size '${adv_param.max_plasmid_size}'

    --min_length '${adv_param.min_length}'  
    --min_rep_evalue '${adv_param.min_rep_evalue}'
    --min_rep_evalue '${adv_param.min_rep_evalue}'
    --min_mob_evalue '${adv_param.min_mob_evalue}'
    --min_con_evalue '${adv_param.min_con_evalue}'
    --min_rep_ident '${adv_param.min_rep_ident}'
    --min_mob_ident '${adv_param.min_mob_ident}'
    --min_con_ident  '${adv_param.min_con_ident}'
    --min_rpp_ident   '${adv_param.min_rpp_ident}'

    --min_rep_cov '${adv_param.min_rep_cov}'
    --min_mob_cov '${adv_param.min_mob_cov}'
    --min_con_cov '${adv_param.min_con_cov}'
    --min_rpp_cov '${adv_param.min_rpp_cov}'
    
    
    --outdir 'outdir' &&
    mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)