diff ipapy2_MS2_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_MS2_annotation.py	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,136 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, MSArgumentParser
+
+
+def main(
+    input_dataset_mapped_isotope_patterns,
+    input_dataset_MS2,
+    input_dataset_adducts,
+    input_dataset_MS2_DB,
+    ppm,
+    ratiosd,
+    ppmunk,
+    ratiounk,
+    ppmthr,
+    pRTNone,
+    pRTout,
+    mzdCS,
+    ppmCS,
+    CSunk,
+    evfilt,
+    output_dataset,
+    ncores,
+):
+    annotations = ipa.MSMSannotation(
+        input_dataset_mapped_isotope_patterns,
+        input_dataset_MS2,
+        input_dataset_adducts,
+        input_dataset_MS2_DB,
+        ppm=ppm,
+        ratiosd=ratiosd,
+        ppmunk=ppmunk,
+        ratiounk=ratiounk,
+        ppmthr=ppmthr,
+        pRTNone=pRTNone,
+        pRTout=pRTout,
+        mzdCS=mzdCS,
+        ppmCS=ppmCS,
+        CSunk=CSunk,
+        evfilt=evfilt,
+        ncores=ncores,
+    )
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+
+if __name__ == "__main__":
+    parser = MSArgumentParser(
+        """Annotation of the dataset base on the MS1 and MS2 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_mapped_isotope_patterns",
+        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_MS2",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing the MS2 fragmentation data",
+    )
+    parser.add_argument(
+        "--input_dataset_adducts",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help=(
+            "A dataset containing the information on all the possible adducts given the"
+            " database. Ideally obtained from compute_all_adducts"
+        ),
+    )
+    parser.add_argument(
+        "--input_dataset_MS2_DB",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="A dataset containing the MS2 database",
+    )
+    parser.add_argument(
+        "--mzdCS",
+        type=int,
+        default=0,
+        help="""maximum mz difference allowed when computing cosine similarity
+           scores. If one wants to use this parameter instead of ppmCS, this
+           must be set to 0. Default 0.""",
+    )
+    parser.add_argument(
+        "--ppmCS",
+        type=int,
+        default=10,
+        help="""maximum ppm allowed when computing cosine similarity scores.
+           If one wants to use this parameter instead of mzdCS, this must be
+           set to 0. Default 10.""",
+    )
+    parser.add_argument(
+        "--CSunk",
+        type=float,
+        default=0.7,
+        help="""cosine similarity score associated with the 'unknown' annotation.
+            Default 0.7""",
+    )
+    parser.add_argument(
+        "--evfilt",
+        type=bool,
+        default=False,
+        help="""Default value False. If true, only spectrum acquired with the same
+            collision energy are considered.""",
+    )
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_MS2,
+        args.input_dataset_adducts,
+        args.input_dataset_MS2_DB,
+        args.ppm,
+        args.ratiosd,
+        args.ppmunk,
+        args.ratiounk,
+        args.ppmthr,
+        args.pRTNone,
+        args.pRTout,
+        args.mzdCS,
+        args.ppmCS,
+        args.CSunk,
+        args.evfilt,
+        args.output_dataset,
+        args.ncores,
+    )