()
| 8 | |
| 9 | |
| 10 | def main(): |
| 11 | |
| 12 | # register command line arguments |
| 13 | model = CTDModel( |
| 14 | name='NameOfThePyTOPPTool', # required |
| 15 | version='1.0', # required |
| 16 | description='This is an example tool how to write pyTOPP tools compatible with the OpenMS workflow ecosystem.', |
| 17 | manual='RTF', |
| 18 | docurl='http://dummy.url/docurl.html', |
| 19 | category='Example', |
| 20 | executableName='exampletool', |
| 21 | executablePath='/path/to/exec/exampletool-1.0/exampletool' |
| 22 | ) |
| 23 | |
| 24 | # Register in / out etc. with CTDModel |
| 25 | model.add( |
| 26 | 'input', |
| 27 | required=True, |
| 28 | type='input-file', |
| 29 | is_list=False, |
| 30 | file_formats=['mzML'], # filename restrictions |
| 31 | description='Input file' |
| 32 | ) |
| 33 | |
| 34 | model.add( |
| 35 | 'output', |
| 36 | required=True, |
| 37 | type='output-file', |
| 38 | is_list=False, |
| 39 | file_formats=['mzML'], # filename restrictions |
| 40 | description='Output file' |
| 41 | ) |
| 42 | |
| 43 | defaults = pms.PeakPickerHiRes().getDefaults() |
| 44 | |
| 45 | # expose algorithm parameters in command line options |
| 46 | addParamToCTDopts(defaults, model) |
| 47 | |
| 48 | # parse command line |
| 49 | # if -write_ini is provided, store model in CTD file, exit with error code 0 |
| 50 | # if -ini is provided, load CTD file into defaults Param object and return new model with paraneters set as defaults |
| 51 | arg_dict, openms_params = parseCTDCommandLine(sys.argv, model, defaults); |
| 52 | |
| 53 | # data processing |
| 54 | fh = pms.MzMLFile() |
| 55 | fh.setLogType(pms.LogType.CMD) |
| 56 | input_map = pms.MSExperiment() |
| 57 | |
| 58 | fh.load(arg_dict["input"], input_map) |
| 59 | |
| 60 | pp = pms.PeakPickerHiRes() |
| 61 | pp.setParameters(openms_params) |
| 62 | out_map = pms.MSExperiment() |
| 63 | pp.pickExperiment(input_map, out_map) |
| 64 | |
| 65 | out_map = addDataProcessing(out_map, openms_params, pms.DataProcessing.ProcessingAction.PEAK_PICKING) |
| 66 | fh = pms.FileHandler() |
| 67 | fh.storeExperiment(arg_dict["output"], out_map) |
no test coverage detected