#import re

## If running in a container use certificates from ca-certificates instead of outdated/missing container certificates
[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
        
datasets download gene $query.subcommand.download_by
#if $query.subcommand.download_by == 'taxon':
    '$query.subcommand.taxon_positional'
#else:
    #if $query.subcommand.text_or_file.text_or_file == 'text':
        #echo " ".join(f"'{x}'" for x in re.split(" |,", str($query.subcommand.text_or_file.accession)) if x)
    #else
        --inputfile '$query.subcommand.text_or_file.inputfile'
    #end if
#end if

#if $query.subcommand.download_by != 'taxon' and $query.subcommand.ortholog:
    --ortholog '$query.subcommand.ortholog'
#end if

#if $query.subcommand.download_by == 'symbol':
    #if $query.subcommand.taxon
        --taxon '$query.subcommand.taxon'
    #end if
#end if

#if $query.subcommand.download_by == 'accession':
    #if $query.subcommand.taxon_filter
        --taxon-filter '$query.subcommand.taxon_filter'
    #end if
    #if str($query.subcommand.include_flanks_bp)
        --include-flanks-bp $query.subcommand.include_flanks_bp
    #end if
#end if

#if $filters.fasta_filter_cond.fasta_filter_select
    #if $filters.fasta_filter_cond.fasta_filter_select == 'text'
        --fasta-filter #echo ",".join(f"'{x}'" for x in $filters.fasta_filter_cond.fasta_filter.split(',') if x)
    #else
        --fasta-filter-file '$filters.fasta_filter_cond.fasta_filter_file'
    #end if
#end if

--include
#if $file_choices.kingdom_cond.include
    #echo ",".join($file_choices.kingdom_cond.include)
#else
    none
#end if

--no-progressbar

## produce TSV report file (either gene or prok-gene)
&& 
dataformat
    tsv
    $file_choices.kingdom_cond.kingdom_sel
    --package ncbi_dataset.zip
    --fields #echo ",".join($file_choices.kingdom_cond.report_columns)
    > gene_data_report.tsv
## if ! dataformat tsv gene --package ncbi_dataset.zip > gene_data_report.tsv 2> dataformat.log; then
##     dataformat tsv prok-gene --package ncbi_dataset.zip > gene_data_report.tsv 2>> dataformat.log;
## fi

#if $file_choices.kingdom_cond.include and "product-report" in $file_choices.kingdom_cond.include
    && dataformat tsv gene-product --package ncbi_dataset.zip > gene_product_report.tsv
#end if

## unzip and rehydrate if any data is to be downloaded (include is not None)
#if $file_choices.kingdom_cond.include
    ## unzip
    && 7z x -y ncbi_dataset.zip > 7z.log
#end if