New tool: TSENAT v.0.99.0

tools/tsenat/.shed.yml

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+name: tsenat
+owner: iuc
+description: TSENAT - Tsallis entropy analysis for transcript-level isoform complexity
+long_description: |
+  TSENAT quantifies isoform-usage complexity in RNA-seq data using Tsallis entropy, detecting coordinate isoform switching
+  and splicing-driven complexity changes that standard differential expression tools (DESeq2, edgeR) miss.
+
+  TSENAT measures the diversity of isoform distributions (entropy) at the gene level, revealing:
+  - Isoforms switching between conditions
+  - Changes in usage distribution complexity
+  - Genes with coordinated or antagonistic isoform patterns
+  - Scale-dependent complexity via the parametric q parameter
+
+  The tool employs multiple statistical methods including SAIT (parametric), Scheirer-Ray-Hare (non-parametric),
+  and Jackknife Isoform Switching (JIS) analysis for robust detection of transcript-level changes.
+homepage_url: https://github.com/gallardoalba/TSENAT
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsenat
+categories:
+  - Transcriptomics
+  - RNA
+  - Statistics
+type: unrestricted

tools/tsenat/macros.xml

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+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.0</token>
+    <token name="@TSENAT_VERSION@">0.99.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TSENAT_VERSION@">r-tsenat</requirement>
+            <requirement type="package" version="1.8.2">r-optparse</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_3308</edam_topic>  <!-- Transcriptomics -->
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_3800</edam_operation>  <!-- RNA-Seq quantification -->
+            <edam_operation>operation_0234</edam_operation>  <!-- Sequence complexity calculation (entropy/diversity) -->
+        </edam_operations>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@software{gallardo2026tsenat,
+  title={TSENAT: Tsallis Entropy Analysis Toolbox},
+  author={Gallardo Alba, Cristóbal},
+  url={https://github.com/gallardoalba/TSENAT},
+  year={2026}
+}</citation>
+        </citations>
+    </xml>
+</macros>

tools/tsenat/test-data/metadata.tsv

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+sample	condition	paired_samples
+SRR14800475	normal	A
+SRR14800476	tumor	A
+SRR14800477	normal	B
+SRR14800478	tumor	B
+SRR14800479	normal	C
+SRR14800480	tumor	C
+SRR14800481	normal	D
+SRR14800482	tumor	D
+SRR14800483	normal	E
+SRR14800484	tumor	E
+SRR14800485	normal	F
+SRR14800486	tumor	F
+SRR14800487	normal	G
+SRR14800488	tumor	G
+SRR14800489	normal	H
+SRR14800490	tumor	H