diff ipapy2_compute_all_adducts.py @ 0:7f84a8a5edde draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_compute_all_adducts.py	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,54 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser
+
+
+def main(
+    input_dataset_adducts, input_dataset_database, ionisation, output_dataset, ncores
+):
+    write_func, file_path = output_dataset
+    adducts_df = ipa.compute_all_adducts(
+        input_dataset_adducts, input_dataset_database, ionisation, ncores
+    )
+
+    write_func(adducts_df, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(
+        description=" Clustering MS1 features based on correlation across samples."
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing information on all possible adducts.",
+    )
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="The MS1 database.",
+    )
+    parser.add_argument(
+        "--ionisation",
+        type=int,
+        default=1,
+        choices=[1, -1],
+        help="Default value 1. positive = 1, negative = -1",
+    )
+    parser.add_argument(
+        "--ncores",
+        type=int,
+        default=1,
+        help="Number of cores to use for parallel processing.",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_adducts,
+        args.input_dataset_database,
+        args.ionisation,
+        args.output_dataset,
+        args.ncores,
+    )