#set $genomic_fasta = ''
        #if str($annotation.annot_choice) == "yes":
            #if str($annotation.fasta_source.fasta_source_selector) == 'history':
                ## Avoid writing FASTA index to inputdir by symlinking 
                ln -s '${$annotation.fasta_source.fasta}' genome.fa &&
                #set $genomic_fasta = 'genome.fa'
            #else
                #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
            #end if
        #end if
        chira_extract.py
        --loci '$loci'
        #if str($annotation.annot_choice) == "yes":
            --gtf '$annotation.gtf'
            #if $hybridize:
                --ref '$genomic_fasta'
            #end if
        #end if
        --tpm_cutoff '$tpm_cutoff'
        --score_cutoff '$score_cutoff'
        --chimeric_overlap '$chimeric_overlap'
        #if str($reference.ref_type) == "single":
            -f1 '$reference.ref_fasta'
        #else if str($reference.ref_type) == "split":
            -f1 '$reference.ref_fasta1'
            -f2 '$reference.ref_fasta2'
        #end if
        $hybridize
        $seed_interaction
        --seed_bp '$seed_bp'
        --seed_min_pu '$seed_min_pu'
        --accessibility '$accessibility'
        --acc_width '$acc_width'
        --intarna_mode '$intarna_mode'
        --temperature $temperature
        $summarize
        --processes "\${GALAXY_SLOTS:-2}"
        --out ./