add wrapper for telogator2

Author: Smeds

tools/telogator2/.shed.yml

@@ -0,0 +1,16 @@
+categories:
+- Sequence Analysis
+- Genomics
+description: Measure allele-specific telomere length from long-read sequencing data
+long_description: |
+  Telogator2 measures allele-specific telomere length (ATL) and characterizes telomere
+  variant repeat (TVR) sequences from PacBio HiFi and Oxford Nanopore long-read sequencing
+  data. The tool identifies individual telomere alleles through TVR characterization,
+  providing chromosome-level resolution of telomere lengths. Supports multiple input
+  formats (FASTA, FASTQ, BAM, CRAM) and includes built-in T2T human reference with
+  support for custom references.
+homepage_url: https://github.com/zstephens/telogator2
+name: telogator2
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator2
+type: unrestricted

tools/telogator2/macros.xml

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+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">telogator2</requirement>
+            <requirement type="package" version="2.28">minimap2</requirement>
+            <requirement type="package" version="2.03">winnowmap</requirement>
+            <requirement type="package" version="1.13.1">pbmm2</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[telogator2 --version]]></version_command>
+    </xml>
+    <token name="@VERSION@">2.2.2</token>
+    <token name="@PROFILE@">24.2</token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0622</edam_topic>
+            <edam_topic>topic_0196</edam_topic>
+            <edam_topic>topic_3673</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_3227</edam_operation>
+            <edam_operation>operation_3192</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">telogator2</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s12859-024-05814-5</citation>
+        </citations>
+    </xml>
+</macros>