os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
# tool type
linker_tool = "Feature Linker Unlabeled QT"
with open(sys.argv[7], "r") as f:
params = xtd.parse(f.read())
for param in params['parameters']['parameter']:
if param['@name'] == "featurelinkerunlabeled.tool_type":
linker_tool = param['#text']
if linker_tool == "Feature Linker Unlabeled QT":
featurelinkerunlabeledqt(in_port, ini_file, out_port)
else:
featurelinkerunlabeledkd(in_port, ini_file, out_port)
fix_filenames(out_port, sys.argv[7])
wrkflw.postvalidation( \
modulename=linker_tool, \
inpath=in_port, \
outpath=out_port, \
logtype=wrkflw.LogType.SINGLE, \
output_per_job=0
)
# command += '-log ' + out_port+'/logfile-00000.txt'
print("COMMAND: " + command + "\n")
os.system(command)
if __name__ == '__main__':
print("===FILE FILTER===")
in_port = sys.argv[4]
out_port = sys.argv[5]
# validate previous module's output
# wrkflw.prevalidation("feature-linker-unlabeled", in_port, logtype="single", output_per_job=0)
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
filefilter(sys.argv[4], sys.argv[5])
wrkflw.postvalidation( \
modulename="file filter", \
inpath=in_port, \
outpath=out_port, \
logtype=wrkflw.LogType.SINGLE, \
output_per_job=1
)
if __name__ == '__main__':
print("===METABOLITE ADDUCT DECHARGER===")
in_port = sys.argv[4]
out_port = sys.argv[6]
# validate previous module's output
# wrkflw.prevalidation("map-aligner-pose-clustering", in_port, logtype="single")
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2] + ":" + os.environ["PATH"]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
metaboliteadductdecharger(in_port, ini_file, out_port)
wrkflw.postvalidation( \
modulename="metabolite adduct decharger", \
inpath=in_port, \
outpath=out_port, \
output_per_job=2
)
# print(sys.argv[1])
# print(sys.argv[2])
# print(sys.argv[3])
# set env
# env = "LD_LIBRARY_PATH="+sys.argv[1] + \
# " PATH="+sys.argv[2] + \
# " OPENMS_DATA_PATH="+sys.argv[3]
# print("env", env)
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = sys.argv[3]
# ini file (argv[5])
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
# parse parameters
in_port = sys.argv[4]
out_port = sys.argv[6]
# execute module
featurefindermetabo(in_port, ini_file, out_port)
wrkflw.postvalidation(modulename="feature finder metabo", inpath=in_port, outpath=out_port)
mpl.run_parallel_shellcommands(commands, 8)
if __name__ == '__main__':
print("===ID Mapper===")
mzml_port = sys.argv[4]
featurefinder_port = sys.argv[7]
out_port = sys.argv[8]
# validate previous module output
# wrkflw.prevalidation("feature-finder-metabo", featurefinder_port)
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
idmapper(mzml_port, ini_file, sys.argv[6], featurefinder_port, out_port)
wrkflw.postvalidation(modulename="id mapper",
inpath=mzml_port,
outpath=out_port)
if __name__ == '__main__':
print("===GNPS EXPORT===")
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
in_port = sys.argv[4]
inputFiles_port = sys.argv[5]
out_port = sys.argv[7]
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
# shutil.copyfile(ini_file, sys.argv[3])
gnpsexport(in_port, inputFiles_port, ini_file, out_port)
wrkflw.postvalidation( \
modulename="gnps export", \
inpath=in_port, \
outpath=out_port, \
logtype=wrkflw.LogType.SINGLE, \
output_per_job=0
)
if __name__ == '__main__':
print("===MAP ALIGNER POSE CLUSTERING===")
in_port = sys.argv[4]
out_port = sys.argv[6]
# validate previous module's output
# wrkflw.prevalidation("id-mapper", in_port)
# set env
os.environ["LD_LIBRARY_PATH"] = sys.argv[1]
os.environ["PATH"] = sys.argv[2]
os.environ["OPENMS_DATA_PATH"] = os.path.abspath(sys.argv[3])
# ini file
ini_file = None
if os.path.exists('iniFiles'):
ini_dir = list(wrkflw.parsefolder('iniFiles'))
if len(ini_dir) > 0:
ini_file = ini_dir[0][0]
mapalignerposeclustering(in_port, ini_file, out_port)
wrkflw.postvalidation(modulename="map aligner pose-clustering", \
inpath=in_port, \
outpath=out_port, \
logtype=wrkflw.LogType.SINGLE
)
