touchbashcli.sh

#!/usr/bin/bash

filename=$1

if [[ $# -eq 0 ]]; then
    echo "Error: no arguments provided"
    echo "USAGE: $(basename $0) [NEW_FILE_NAME]"
    exit 1
fi

touch ${filename}.sh
chmod u+x ${filename}.sh

# Guts of template
template() {
    cat <<'EOF'
#!/usr/bin/bash

# AUTHOR: James Lingford (james.lingford@monash.edu)
# DESC: A bash script to add annotations to protein fasta headers from a .tsv file

# -------------------------------------------
# init vars

input1=""          # path to input file1
input2=""          # path to input file2
param1=""          # column of interest to map info to faafile headers

# -------------------------------------------
# helper functions

usage="USAGE: $(basename "$0") [-h] -i input1 -d input2

DESCRIPTION:

OPTIONS:
    -i  path to input (required)
    -d  path to input (required)
    -h  show this help text

REQUIRES: seqkit

EXAMPLE USAGE:
$(basename $0) -i path/to/tsv.tsv -d path/to/tsv2.tsv > path/to/new_faa_file

"

# print help anyway if no args provided
if [[ $# -eq 0 ]]; then
    echo "$usage"
    exit 1
fi

# getops stuff
while getopts 'i:d:h' option; do
    case "$option" in
    h)
        echo "$usage"
        exit
        ;;
    i)
        input1=$OPTARG
        ;;
    d)
        input2=$OPTARG
        ;;
    \?)
        printf "[WARNING]: illegal option: -%s\n" "$OPTARG" >&2
        echo "For help, see: $(basename $0) -h"
        exit 1
        ;;
    esac
done
shift $((OPTIND - 1))

# -------------------------------------------
# sanity checks

# check all vars are set
if [[ -z "$input1" || -z "$input2" ]]; then
    echo "[WARNING]: some options not set."
    echo "For help, see: $(basename $0) -h"
    exit 1
fi

# check input files acutally exist
if [[ ! -f "$input1" || ! -f "$input2" ]]; then
    echo "[WARNING]: the .tsv or .faa file does not exist. Double check input filepaths"
    echo "For help, see: $(basename $0) -h"
    exit 1
fi

# check that DEPENDENCY is installed and on PATH
if ! command -v seqkit &>/dev/null; then
    echo "[WARNING]: seqkit not found on PATH"
    echo "See seqkit installation docs: https://bioinf.shenwei.me/seqkit/download/#installation"
    exit 1
fi

# -------------------------------------------
# main function


EOF
}

template >"${filename}.sh"