Mercurial > repos > recetox > ramclustr_define_experiment

annotate ramclustr_define_experiment_wrapper.py @ 0:42c2a25ff197 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
author recetox
date Wed, 29 Jun 2022 10:00:43 +0000
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42c2a25ff197 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
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1 import argparse
42c2a25ff197 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
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2 import csv
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3 import sys
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6 ARGUMENTS = {
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7 "Experiment": {"help": "Experiment name, no spaces.", "type": str},
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8 "Species": {"help": "Genus species from which samples are derived.", "type": str},
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9 "Sample": {"help": "Type of sample (e.g., serum, leaf).", "type": str},
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10 "Contributer": {"help": "Your or your PI's name.", "type": str},
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11 "platform": {"help": "Either GC-MS or LC-MS.", "type": str},
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12 "chrominst": {"help": "Model of LC/GC instrument.", "type": str},
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13 "msinst": {"help": "Model of MS instrument.", "type": str},
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14 "column": {"help": "Column description.", "type": str},
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15 "InletTemp": {"help": "Temperature of inlet.", "type": str},
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16 "TransferTemp": {"help": "Temperature of GC to MS transfer line.", "type": str},
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17 "mstype": {"help": "Type of mass spectrometer (one of QQQ, TOF, QTOF, Orbi, Q).", "type": str},
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18 "msmode": {"help": "Positive or negative ion mode.", "type": str},
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19 "ionization": {"help": "Ionization (EI, AP, or CI).", "type": str},
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20 "msscanrange": {"help": "Scan range used for acquisition.", "type": str},
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21 "scantime": {"help": "Time for each full scan spectrum (e.g. 0.2 seconds).", "type": float},
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22 "deriv": {"help": "Derivitization (TMS, TBDMS, or None).", "type": str},
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23 "MSlevs": {"help": "Number of levels of energy acquired - 1 typically.", "type": float},
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24 "solvA": {"help": "Solvent A composition.", "type": str},
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25 "solvB": {"help": "Solvent B composition.", "type": str},
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26 "CE1": {"help": "Collision energy of acquisition of MS data.", "type": str},
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27 "CE2": {"help": "Collision energy of acquisition for MSe/idMSMS data (when applicable).", "type": str},
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28 "colgas": {"help": "Gas used for collisional dissociation.", "type": str},
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29 "conevol": {"help": "Cone voltage used for acquisition.", "type": str}
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30 }
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33 def get_value(args, value, fill=True):
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34 if fill:
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35 return args[value]
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36 return "fill"
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39 def write_gcms(csv_writer, args, fill=True):
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40 csv_writer.writerow(["", "", ""])
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41 csv_writer.writerow(["GC-MS", "", ""])
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43 gcms = ["chrominst", "msinst", "column", "InletTemp", "TransferTemp", "mstype", "msmode", "ionization",
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44 "msscanrange", "scantime", "deriv", "MSlevs"]
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45 for arg in gcms:
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46 csv_writer.writerow([arg, get_value(args, arg, fill=fill), ARGUMENTS[arg]["help"]])
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49 def write_lcms(csv_writer, args, fill=True):
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50 csv_writer.writerow(["", "", ""])
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51 csv_writer.writerow(["LC-MS", "", ""])
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52
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53 lcms = ["chrominst", "msinst", "column", "solvA", "solvB", "CE1", "CE2", "mstype", "msmode", "ionization", "colgas",
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54 "msscanrange", "conevol", "MSlevs"]
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55 for arg in lcms:
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56 csv_writer.writerow([arg, get_value(args, arg, fill=fill), ARGUMENTS[arg]["help"]])
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58
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59 def main(argv):
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60 parser = argparse.ArgumentParser(description="RAMClustR define experiment.")
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61
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62 for arg in ARGUMENTS.keys():
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63 parser.add_argument(f"--{arg}", type=ARGUMENTS[arg]["type"], help=ARGUMENTS[arg]["help"])
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64
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65 parser.add_argument("--output_file", type=str, help="Path to output csv file.")
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66 args = vars(parser.parse_args())
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67
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68 with open(args["output_file"], "w") as csvfile:
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69 csv_writer = csv.writer(csvfile, delimiter=',')
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70
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71 csv_writer.writerow(["parameter", "Value", "Description"])
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72 csv_writer.writerow(["", "", ""])
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73 csv_writer.writerow(["Experimental Design", "", ""])
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74
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75 general = ["Experiment", "Species", "Sample", "Contributer", "platform"]
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76 for arg in general:
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77 csv_writer.writerow([arg, args[arg], ARGUMENTS[arg]["help"]])
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78
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79 if args["platform"] == "GC-MS":
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80 write_gcms(csv_writer, args)
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81 write_lcms(csv_writer, args, fill=False)
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82 elif args["platform"] == "LC-MS":
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83 write_gcms(csv_writer, args, fill=False)
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84 write_lcms(csv_writer, args)
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85 else:
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86 raise ValueError("Platform value incorrect, choose either GC-MS or LC-MS.")
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87
42c2a25ff197 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
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parents:
diff changeset
88
42c2a25ff197 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
recetox
parents:
diff changeset
89 if __name__ == "__main__":
42c2a25ff197 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
recetox
parents:
diff changeset
90 main(argv=sys.argv[1:])