export PYTHONWARNINGS="ignore::FutureWarning" &&

        #import os, glob
        #set $htmloutputfolder = $html.files_path
        #if str($infile.ext) == 'genbank':
            #set $file_extension = 'gb'
        #else:
            #set $file_extension = $infile.ext
        #end if

        ln -s '$infile' input_tempfile.$file_extension &&
        #if $genefinding_gff3
            ln -s $genefinding_gff3 annotation.gff3 &&
        #end if

        #if $sideload.file
            #if $sideload.format == 'harmonize'
                python '$__tool_directory__/harmonize2antismash.py' '$sideload.file' sideload.json &&
            #else
                ln -s '$sideload.file' sideload.json &&
            #end if
        #end if

        ## create html folder
        mkdir -p '$htmloutputfolder' &&

        antismash
            --cpus "\${GALAXY_SLOTS:-12}"
            --taxon '${cond_taxon.taxon}'
            #if $genefinding_gff3
                --genefinding-gff3 annotation.gff3
            #end if
            --genefinding-tool $cond_taxon.genefinding_tool

            ${cb_general}
            ${cb_subclusters}
            ${cb_knownclusters}
            ${smcog_trees}
            --tta-threshold ${tta_threshold}
            ${asf}

            ${clusterhmmer}
            ${fullhmmer}
            #if $cond_taxon.taxon == 'fungi':
                $cond_taxon.cassis
            #else   
                $cond_taxon.tigrfam
            #end if

            ${cc_mibig}
            ${rre}
            --logfile $log

            ## Advanced options
            --minlength $advanced_options.minlength
            --hmmdetection-strictness $advanced_options.hmmdetection_strictness
            --cb-nclusters $advanced_options.cb_nclusters
            --cb-min-homology-scale $advanced_options.cb_min_homology_scale
            --rre-cutoff $advanced_options.rre_cutoff
            --rre-minlength $advanced_options.rre_minlength

            #if $sideload.file
                --sideload 'sideload.json'
            #end if

            input_tempfile.$file_extension &&

        ## copy all content to html folder
        cp input_tempfile/index.html '${html}' 2> /dev/null &&
        cp -r input_tempfile/* '${htmloutputfolder}'