added type map for collate of allele annotations

bokulich-lab · Mar 20, 2024 · e8203ad · e8203ad
1 parent aafb201
commit e8203ad
Showing 1 changed file with 28 additions and 2 deletions.
diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
@@ -246,11 +246,37 @@
     "and collates them into a single artifact.",
 )
 
+T_allele_annotation_collate_in, T_allele_annotation_collate_out = TypeMap(
+    {
+        List[
+            SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa")]
+        ]: SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2", "bwa")],
+        List[
+            SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2")]
+        ]: SampleData[CARDAlleleAnnotation % Properties("kma", "bowtie2")],
+        List[SampleData[CARDAlleleAnnotation % Properties("kma", "bwa")]]: SampleData[
+            CARDAlleleAnnotation % Properties("kma", "bwa")
+        ],
+        List[
+            SampleData[CARDAlleleAnnotation % Properties("bowtie2", "bwa")]
+        ]: SampleData[CARDAlleleAnnotation % Properties("bowtie2", "bwa")],
+        List[SampleData[CARDAlleleAnnotation % Properties("kma")]]: SampleData[
+            CARDAlleleAnnotation % Properties("kma")
+        ],
+        List[SampleData[CARDAlleleAnnotation % Properties("bowtie2")]]: SampleData[
+            CARDAlleleAnnotation % Properties("bowtie2")
+        ],
+        List[SampleData[CARDAlleleAnnotation % Properties("bwa")]]: SampleData[
+            CARDAlleleAnnotation % Properties("bwa")
+        ],
+    }
+)
+
 plugin.methods.register_function(
     function=collate_reads_allele_annotations,
-    inputs={"annotations": List[SampleData[CARDAlleleAnnotation]]},
+    inputs={"annotations": T_allele_annotation_collate_in},
     parameters={},
-    outputs={"collated_annotations": SampleData[CARDAlleleAnnotation]},
+    outputs={"collated_annotations": T_allele_annotation_collate_out},
     input_descriptions={
         "annotations": "A collection of annotations from reads at "
         "allele level to be collated."