INNER CODE UNIT · Shell

showhelp

pirovc/genome_updater · genome_updater.sh:956

function showhelp
{
    echo
    echo $'Source:'
    echo $' -d Database(s) (comma-separated, mandatory)'
    echo $'\tOptions: "genbank, refseq"'
    echo $'\tDefault: ""'
    echo $' -f File type(s) to download (comma-separated, mandatory)'
    echo $'\tOptions: "genomic.fna.gz, assembly_report.txt, protein.faa.gz, genomic.gbff.gz, ..." all available formats are described at https://ftp.ncbi.nlm.nih.gov/genomes/all/README.txt'
    echo $'\tDefault: "assembly_report.txt"'
    echo
    echo $'Organism/Taxa:'
    echo $' -g Organism group(s) (comma-separated, empty for all)'
    echo $'\tOptions: "archaea, bacteria, fungi, human, invertebrate, metagenomes, other, plant, protozoa, vertebrate_mammalian, vertebrate_other, viral"'
    echo $'\tDefault: ""'
    echo $' -T Taxonomic group(s) (comma-separated, empty for all)'
    echo $'\tOptional negation using the ^ prefix.'
    echo $'\tExample: "543,^562" (for -M ncbi) or "f__Enterobacteriaceae,^s__Escherichia coli" (for -M gtdb)'

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