diff ipapy2_compute_bio.py @ 0:6a23970e8093 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_bio.py	Fri May 16 08:01:15 2025 +0000
@@ -0,0 +1,87 @@
+from ipaPy2 import ipa
+from utils import CustomArgumentParser, group_by_peak_id
+
+
+def main(
+    input_dataset_database,
+    input_dataset_annotations,
+    biochemical_mode,
+    connection_list,
+    output_dataset,
+    ncores,
+):
+    """
+    Compute matrix of biochemical connections. Either based on a list of
+    possible connections in the form of a list of formulas or based on the
+    reactions present in the database.
+    """
+
+    if input_dataset_annotations is not None:
+        annotations = group_by_peak_id(input_dataset_annotations)
+    else:
+        annotations = None
+
+    if biochemical_mode == "connections" and connection_list:
+        connections = connection_list.split(",")
+    else:
+        connections = []
+
+    Bio = ipa.Compute_Bio(
+        input_dataset_database,
+        annotations=annotations,
+        mode=biochemical_mode,
+        connections=connections,
+        ncores=ncores,
+    )
+    write_func, file_path = output_dataset
+    write_func(Bio, file_path)
+
+
+if __name__ == "__main__":
+    parser = CustomArgumentParser(
+        description=""" Compute matrix of biochemical connections. Either based on a list of
+    possible connections in the form of a list of formulas or based on the
+    reactions present in the database."""
+    )
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "a datset containing the database against which the annotationis performed."
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_annotations",
+        nargs=2,
+        action="load_data",
+        help="a datset containing the annotations of the features.",
+    )
+    parser.add_argument(
+        "--biochemical_mode",
+        type=str,
+        required=True,
+        help="""either 'reactions' (connections are computed based on the reactions
+          present in the database) or 'connections' (connections are computed
+          based on the list of connections provided). Default 'reactions'. """,
+    )
+    parser.add_argument(
+        "--connection_list", type=str, help="list of connections"
+    )
+    parser.add_argument(
+        "--ncores",
+        type=int,
+        default=None,
+        help="number of cores to use for the computation.",
+    )
+    args = parser.parse_args()
+
+    main(
+        args.input_dataset_database,
+        args.input_dataset_annotations,
+        args.biochemical_mode,
+        args.connection_list,
+        args.output_dataset,
+        args.ncores,
+    )