quartet-protqc-report/resources/bin/protqc.sh

#!/usr/bin/env bash

# A wrapper for protqc r package
#
# Author: Jingcheng Yang
# Email: yjcyxky@163.com
#
# License: MIT

# Exit on error. Append "|| true" if you expect an error.
# set -o errexit
# Exit on error inside any functions or subshells.
# set -o errtrace
# Do not allow use of undefined vars. Use ${VAR:-} to use an undefined VAR
set -o nounset
# Catch the error in case mysqldump fails (but gzip succeeds) in `mysqldump |gzip`
set -o pipefail
# Turn on traces, useful while debugging but commented out by default
# set -o xtrace

show_help() {
	cat <<EOF
usage: $(echo $0) [-d <DATA_FILE>] [-m <META_FILE>] [-o <RESULT_DIR>]
       -d DATA_FILE Proteomics profiled data.
       -m META_FILE Metadata file.
       -o RESULT_DIR A directory for result files.
EOF
}

while getopts ":hd:m:o:" arg; do
	case "$arg" in
	"d")
		DATA_FILE="$OPTARG"
		;;
	"m")
		META_FILE="$OPTARG"
		;;
	"o")
		RESULT_DIR="$OPTARG"
		;;
	"?")
		echo "Unkown option: $OPTARG"
		exit 1
		;;
	":")
		echo "No argument value for option $OPTARG"
		;;
	h)
		show_help
		exit 0
		;;
	*)
		echo "Unknown error while processing options"
		show_help
		exit 1
		;;
	esac
done

if [ -z "$DATA_FILE" ]; then
	echo "-d argument is not specified."
	exit 1
elif [ ! -f "$DATA_FILE" ]; then
	echo "$DATA_FILE is not a valid file."
	exit 1
else
	DATA_FILE=$(realpath $DATA_FILE)
fi

if [ -z "$META_FILE" ]; then
	echo "-m argument is not specified."
	exit 1
elif [ ! -f "$META_FILE" ]; then
	echo "$META_FILE is not a valid file."
	exit 1
else
	META_FILE=$(realpath $META_FILE)
fi

if [ -z "$RESULT_DIR" ]; then
	echo "-o argument is not specified."
	exit 1
elif [ ! -d "$RESULT_DIR" ]; then
	echo "$RESULT_DIR is not a valid directory."
	exit 1
else
	RESULT_DIR=$(realpath $RESULT_DIR)
fi

TEMP=$(mktemp)

echo "Run script: $TEMP"

cat <<EOF >"$TEMP"
#!/usr/bin/env Rscript

run <- function() {
	# Print traceback message
	on.exit(traceback())
	library(ProtQC)
	print("Running...")
	ProtQC::plot_pca("$DATA_FILE", "$META_FILE", "$RESULT_DIR")
  ProtQC::plot_corr("$DATA_FILE", "$META_FILE", "$RESULT_DIR")
  ProtQC::table_conclusion("$DATA_FILE", "$META_FILE", "$RESULT_DIR")
}

run()
EOF

printf "\n---------------------\n"
cat "$TEMP"
echo "---------------------"

Rscript $TEMP