Mercurial > repos > recetox > ramclustr_define_experiment
view ramclustr_define_experiment_wrapper.py @ 3:049285068dad draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
author | recetox |
---|---|
date | Thu, 22 Jun 2023 11:45:32 +0000 |
parents | 42c2a25ff197 |
children |
line wrap: on
line source
import argparse import csv import sys ARGUMENTS = { "Experiment": {"help": "Experiment name, no spaces.", "type": str}, "Species": {"help": "Genus species from which samples are derived.", "type": str}, "Sample": {"help": "Type of sample (e.g., serum, leaf).", "type": str}, "Contributer": {"help": "Your or your PI's name.", "type": str}, "platform": {"help": "Either GC-MS or LC-MS.", "type": str}, "chrominst": {"help": "Model of LC/GC instrument.", "type": str}, "msinst": {"help": "Model of MS instrument.", "type": str}, "column": {"help": "Column description.", "type": str}, "InletTemp": {"help": "Temperature of inlet.", "type": str}, "TransferTemp": {"help": "Temperature of GC to MS transfer line.", "type": str}, "mstype": {"help": "Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q).", "type": str}, "msmode": {"help": "Positive or negative ion mode.", "type": str}, "ionization": {"help": "Ionization (EI, AP, or CI).", "type": str}, "msscanrange": {"help": "Scan range used for acquisition.", "type": str}, "scantime": {"help": "Time for each full scan spectrum (e.g. 0.2 seconds).", "type": float}, "deriv": {"help": "Derivitization (TMS, TBDMS, or None).", "type": str}, "MSlevs": {"help": "Number of levels of energy acquired - 1 typically.", "type": float}, "solvA": {"help": "Solvent A composition.", "type": str}, "solvB": {"help": "Solvent B composition.", "type": str}, "CE1": {"help": "Collision energy of acquisition of MS data.", "type": str}, "CE2": {"help": "Collision energy of acquisition for MSe/idMSMS data (when applicable).", "type": str}, "colgas": {"help": "Gas used for collisional dissociation.", "type": str}, "conevol": {"help": "Cone voltage used for acquisition.", "type": str} } def get_value(args, value, fill=True): if fill: return args[value] return "fill" def write_gcms(csv_writer, args, fill=True): csv_writer.writerow(["", "", ""]) csv_writer.writerow(["GC-MS", "", ""]) gcms = ["chrominst", "msinst", "column", "InletTemp", "TransferTemp", "mstype", "msmode", "ionization", "msscanrange", "scantime", "deriv", "MSlevs"] for arg in gcms: csv_writer.writerow([arg, get_value(args, arg, fill=fill), ARGUMENTS[arg]["help"]]) def write_lcms(csv_writer, args, fill=True): csv_writer.writerow(["", "", ""]) csv_writer.writerow(["LC-MS", "", ""]) lcms = ["chrominst", "msinst", "column", "solvA", "solvB", "CE1", "CE2", "mstype", "msmode", "ionization", "colgas", "msscanrange", "conevol", "MSlevs"] for arg in lcms: csv_writer.writerow([arg, get_value(args, arg, fill=fill), ARGUMENTS[arg]["help"]]) def main(argv): parser = argparse.ArgumentParser(description="RAMClustR define experiment.") for arg in ARGUMENTS.keys(): parser.add_argument(f"--{arg}", type=ARGUMENTS[arg]["type"], help=ARGUMENTS[arg]["help"]) parser.add_argument("--output_file", type=str, help="Path to output csv file.") args = vars(parser.parse_args()) with open(args["output_file"], "w") as csvfile: csv_writer = csv.writer(csvfile, delimiter=',') csv_writer.writerow(["parameter", "Value", "Description"]) csv_writer.writerow(["", "", ""]) csv_writer.writerow(["Experimental Design", "", ""]) general = ["Experiment", "Species", "Sample", "Contributer", "platform"] for arg in general: csv_writer.writerow([arg, args[arg], ARGUMENTS[arg]["help"]]) if args["platform"] == "GC-MS": write_gcms(csv_writer, args) write_lcms(csv_writer, args, fill=False) elif args["platform"] == "LC-MS": write_gcms(csv_writer, args, fill=False) write_lcms(csv_writer, args) else: raise ValueError("Platform value incorrect, choose either GC-MS or LC-MS.") if __name__ == "__main__": main(argv=sys.argv[1:])