def _check_toolplus(x):
"""Parse options for adding non-standard/commercial tools like GATK and MuTecT.
"""
import argparse
Tool = collections.namedtuple("Tool", ["name", "fname"])
std_choices = set(["data", "cadd", "dbnsfp"])
if x in std_choices:
return Tool(x, None)
elif "=" in x and len(x.split("=")) == 2:
name, fname = x.split("=")
fname = os.path.normpath(os.path.realpath(fname))
if not os.path.exists(fname):
raise argparse.ArgumentTypeError("Unexpected --toolplus argument for %s. File does not exist: %s"
% (name, fname))
return Tool(name, fname)
else:
raise argparse.ArgumentTypeError("Unexpected --toolplus argument. Expect toolname=filename.")
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