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add wrapper for telogator2 #7481

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cc172e9
add wrapper for telogator2
Smeds Nov 21, 2025
1386697
handle review comments and fix failing tests
Smeds Dec 1, 2025
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15 changes: 15 additions & 0 deletions tools/telogator2/.shed.yml
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categories:
- Sequence Analysis
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
37 changes: 37 additions & 0 deletions 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>
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