--- a
+++ b/tools/argparse.bash
@@ -0,0 +1,103 @@
+#!/usr/bin/env bash
+
+# Use python's argparse module in shell scripts
+#
+# The function `argparse` parses its arguments using
+# argparse.ArgumentParser; the parser is defined in the function's
+# stdin.
+#
+# Executing ``argparse.bash`` (as opposed to sourcing it) prints a
+# script template.
+#
+# https://github.com/nhoffman/argparse-bash
+# MIT License - Copyright (c) 2015 Noah Hoffman
+#
+# The MIT License (MIT)
+#
+# Copyright (c) 2015 Noah Hoffman
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+argparse(){
+    argparser=$(mktemp 2>/dev/null || mktemp -t argparser)
+    cat > "$argparser" <<EOF
+from __future__ import print_function
+import argparse
+import os
+import sys
+
+
+class MyArgumentParser(argparse.ArgumentParser):
+    def print_help(self, file=None):
+        """Print help and exit with error"""
+        super(MyArgumentParser, self).print_help(file=file)
+        sys.exit(1)
+
+parser = MyArgumentParser(prog=os.path.basename("$0"),
+            description="""$ARGPARSE_DESCRIPTION""")
+EOF
+
+    # stdin to this function should contain the parser definition
+    cat >> "$argparser"
+
+    cat >> "$argparser" <<EOF
+args = parser.parse_args()
+for arg in [a for a in dir(args) if not a.startswith('_')]:
+    key = arg.upper()
+    value = getattr(args, arg, None)
+
+    if isinstance(value, bool) or value is None:
+        print('{0}="{1}";'.format(key, 'yes' if value else ''))
+    elif isinstance(value, list):
+        print('{0}=({1});'.format(key, ' '.join('"{0}"'.format(s) for s in value)))
+    else:
+        print('{0}="{1}";'.format(key, value))
+EOF
+
+    # Define variables corresponding to the options if the args can be
+    # parsed without errors; otherwise, print the text of the error
+    # message.
+    if python "$argparser" "$@" &> /dev/null; then
+        eval $(python "$argparser" "$@")
+        retval=0
+    else
+        python "$argparser" "$@"
+        retval=1
+    fi
+
+    rm "$argparser"
+    return $retval
+}
+
+# print a script template when this script is executed
+if [[ $0 == *argparse.bash ]]; then
+    cat <<FOO
+#!/usr/bin/env bash
+
+source \$(dirname \$0)/argparse.bash || exit 1
+argparse "\$@" <<EOF || exit 1
+parser.add_argument('infile')
+parser.add_argument('-o', '--outfile')
+
+EOF
+
+echo "INFILE: \${INFILE}"
+echo "OUTFILE: \${OUTFILE}"
+FOO
+fi