diff ipapy2_gibbs_sampler_add.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_gibbs_sampler_add.py	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,76 @@
+from ipaPy2 import ipa
+from utils import flattern_annotations, GibbsArgumentParser, group_by_peak_id
+
+
+def main(
+    mapped_isotope_patterns,
+    annotations_df,
+    noits,
+    burn,
+    delta_add,
+    all_out,
+    zs,
+    zs_out,
+    output_dataset,
+):
+    df = mapped_isotope_patterns
+
+    annotations_df = annotations_df
+    annotations_df["post"] = annotations_df["post"].replace("", 0)
+    annotations_df = annotations_df.replace("", None)
+    annotations = group_by_peak_id(annotations_df)
+
+    if not zs:
+        zs = None
+
+    zs = ipa.Gibbs_sampler_add(
+        df,
+        annotations,
+        noits=noits,
+        burn=burn,
+        delta_add=delta_add,
+        all_out=all_out,
+        zs=zs,
+    )
+
+    annotations_flat = flattern_annotations(annotations)
+    write_func, file_path = output_dataset
+    write_func(annotations_flat, file_path)
+
+    if all_out:
+        write_func, file_path = zs_out
+        write_func(zs, file_path)
+
+
+if __name__ == "__main__":
+    parser = GibbsArgumentParser(description="cluster features before IPA pipeline.")
+    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_annotations",
+        nargs=2,
+        action="load_data",
+        required=True,
+        help="a datset containing the annotations of the features.",
+    )
+
+    args = parser.parse_args()
+    main(
+        args.input_dataset_mapped_isotope_patterns,
+        args.input_dataset_annotations,
+        args.noits,
+        args.burn,
+        args.delta_add,
+        args.all_out,
+        args.zs,
+        args.zs_out,
+        args.output_dataset,
+    )