comparison tools/effectiveT3/effectiveT3.py @ 29:35c358aa7801 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty

28:d6976a4c055b

effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")

if "-v" in sys.argv or "--version" in sys.argv:
    # TODO - Get version of the JAR file dynamically?
    print("Wrapper v0.0.17, TTSS_GUI-1.0.1.jar")
    sys.exit(0)

if len(sys.argv) != 5:
    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")

    """Run the command line string via subprocess."""
    # Avoid using shell=True when we call subprocess to ensure if the Python
    # script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception, err:
        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    # Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code or stderr.startswith("Exception in thread"):

29:35c358aa7801

effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
effective_t3_jar = os.path.join(effective_t3_dir, "TTSS_GUI-1.0.1.jar")

if "-v" in sys.argv or "--version" in sys.argv:
    # TODO - Get version of the JAR file dynamically?
    print("Wrapper v0.0.19, TTSS_GUI-1.0.1.jar")
    sys.exit(0)

if len(sys.argv) != 5:
    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")

    """Run the command line string via subprocess."""
    # Avoid using shell=True when we call subprocess to ensure if the Python
    # script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception as err:
        sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    # Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code or stderr.startswith("Exception in thread"):