assembly_stats_txt.py does not return error code

[peterjc]

Currently code is:

https://github.com/phac-nml/galaxy_tools/blob/master/tools/assemblystats/assembly_stats_txt.py#L18

def stop_err(msg):
    sys.stderr.write('%s\n' % msg)
    sys.exit()

This will return a zero exit level, i.e. no error will be report by Galaxy.

Quick fix:

def stop_err(msg):
    sys.stderr.write('%s\n' % msg)
    sys.exit(1)

Better fix, replace all calls to stop_err with sys.exit which will accept a string, print this to stderr, and exit with return code one.

[mgopez]

Addressed in #193
Returns the actual exit code from the .pl script, and the output as well.