diff ipapy2_MS1_annotation.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_MS1_annotation.py	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,73 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, MSArgumentParser
+
+
+def main(
+    input_dataset_database,
+    input_dataset_adduct,
+    ppm,
+    ratiosd,
+    ppmunk,
+    ratiounk,
+    ppmthr,
+    pRTNone,
+    pRTout,
+    output_dataset,
+    ncores,
+):
+    write_func, file_path = output_dataset
+
+    annotations = ipa.MS1annotation(
+        input_dataset_database,
+        input_dataset_adduct,
+        ppm=ppm,
+        ratiosd=ratiosd,
+        ppmunk=ppmunk,
+        ratiounk=ratiounk,
+        ppmthr=ppmthr,
+        pRTNone=pRTNone,
+        pRTout=pRTout,
+        ncores=ncores,
+    )
+    annotations_flat = flattern_annotations(annotations)
+    write_func(annotations_flat, file_path)
+
+
+if __name__ == "__main__":
+    parser = MSArgumentParser("""
+    Annotation of the dataset based on the MS1 information. Prior probabilities
+        are based on mass only, while post probabilities are based on mass, RT,
+        previous knowledge and isotope patterns.
+    """)
+    parser.add_argument(
+        "--input_dataset_database",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the MS1 data. Ideally obtained from"
+            " map_isotope_patterns"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing information on all possible adducts.",
+    )
+
+    args = parser.parse_args()
+    main(
+        args.input_dataset_database,
+        args.input_dataset_adducts,
+        args.ppm,
+        args.ratiosd,
+        args.ppmunk,
+        args.ratiounk,
+        args.ppmthr,
+        args.pRTNone,
+        args.pRTout,
+        args.output_dataset,
+        args.ncores,
+    )