Mercurial > repos > recetox > ipapy2_ms1_annotation
comparison ipapy2_clustering.py @ 0:7f84a8a5edde draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
| author | recetox |
|---|---|
| date | Fri, 16 May 2025 08:00:41 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:7f84a8a5edde |
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| 1 from ipaPy2 import ipa | |
| 2 from utils import CustomArgumentParser | |
| 3 | |
| 4 | |
| 5 def main(input_dataset, Cthr, RTwin, Intmode, output_dataset): | |
| 6 write_func, file_path = output_dataset | |
| 7 clustered_df = ipa.clusterFeatures( | |
| 8 input_dataset, Cthr=Cthr, RTwin=RTwin, Intmode=Intmode | |
| 9 ) | |
| 10 write_func(clustered_df, file_path) | |
| 11 | |
| 12 | |
| 13 if __name__ == "__main__": | |
| 14 parser = CustomArgumentParser( | |
| 15 description=" Clustering MS1 features based on correlation across samples." | |
| 16 ) | |
| 17 parser.add_argument( | |
| 18 "--input_dataset", | |
| 19 nargs=2, | |
| 20 action="load_data", | |
| 21 required=True, | |
| 22 help="The unclustered MS1 intensities file path.", | |
| 23 ) | |
| 24 | |
| 25 parser.add_argument( | |
| 26 "--Cthr", | |
| 27 type=float, | |
| 28 default=0.8, | |
| 29 help="Minimum correlation allowed in each cluster. Default value 0.8.", | |
| 30 ) | |
| 31 | |
| 32 parser.add_argument( | |
| 33 "--RTwin", | |
| 34 type=float, | |
| 35 default=1, | |
| 36 help=( | |
| 37 "Maximum difference in RT time between features in the same cluster." | |
| 38 " Default value 1." | |
| 39 ), | |
| 40 ) | |
| 41 | |
| 42 parser.add_argument( | |
| 43 "--Intmode", | |
| 44 type=str, | |
| 45 default="max", | |
| 46 choices=["max", "ave"], | |
| 47 help="intensity mode. Default 'max' or 'ave'.", | |
| 48 ) | |
| 49 args = parser.parse_args() | |
| 50 main(args.input_dataset, args.Cthr, args.RTwin, args.Intmode, args.output_dataset) |