Mercurial > repos > galaxyp > msconvert_nix
diff msconvert_wrapper.py @ 1:b00023193f6e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
author | galaxyp |
---|---|
date | Tue, 14 Mar 2017 16:45:13 -0400 |
parents | 5f8848c7d7b7 |
children |
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--- a/msconvert_wrapper.py Fri Apr 08 15:46:25 2016 -0400 +++ b/msconvert_wrapper.py Tue Mar 14 16:45:13 2017 -0400 @@ -7,6 +7,7 @@ import subprocess import re import logging +import shlex assert sys.version_info[:2] >= (2, 6) @@ -40,7 +41,8 @@ try: with open(tmp_stderr_name, 'wb') as tmp_stderr: with open(tmp_stdout_name, 'wb') as tmp_stdout: - proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) + args = shlex.split(command) # handle proper splitting of quoted args + proc = subprocess.Popen(args=args, shell=False, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) returncode = proc.wait() if returncode != 0: raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))