ExplorATE

#!/bin/bash
BINDIR=$(dirname `readlink -f $0`) && export BINDIR=${BINDIR}/bin
green=`tput setaf 2`
yellow=`tput setaf 3`
reset=`tput sgr0`

# version #
export ExplorATE_VERSION=0.0.1

# usage #
usage (){
echo "${green}=============================
${yellow}|||       ExplorATE       |||
${green}=============================${reset}"
echo "Version ${ExplorATE_VERSION}"

echo "Usage:
ExplorATE ${yellow}[mode] ${green}[flags]${reset}
modes:"
echo -e "\tExplorATE ${yellow}mo${reset} <model organisms analysis>"
echo -e "\tExplorATE ${yellow}nmo${reset} <run the pipeline for non-model organisms from user generated files>"
echo -e "\tExplorATE ${yellow}nmo_in${reset} <generates input files only (e.g. to use in R)>"
echo -e "\tExplorATE ${yellow}nmo_all${reset} <run all pipeline for non-model organisms (generating intermediate annotation files)>"
echo "run ExplorATE ${yellow}[mode]${reset} -h to see flags for each mode"
}

# run #
if [ $# -lt 1 ];then
	usage
	exit 1
fi
case ${1} in
	mo)
		shift && bash ${BINDIR}/ExplorATE_mo.sh "$@";;
	nmo)
		shift && bash ${BINDIR}/ExplorATE_nmo_with_user_inputs.sh "$@";;
	nmo_in)
		shift && bash ${BINDIR}/ExplorATE_nmo_generate_inputs.sh "$@";;
	nmo_all)
		shift && bash ${BINDIR}/ExplorATE_nmo_all.sh "$@";;
	*)
		usage;;
esac