Add Snapatac2 wrappers (galaxyproject#5740)

* Add Snapatac2 wrappers

* add test data

* updated tools

* Fix some tests

* update tools

* update

* added metrics.tsse to preprocessing.xml

* tests tutorial1

* added tl.umap test

* fix tl.umap by setting NUMBA_CACHE_DIR variable

* add .shed.yaml

* add location for large files

* delete test data larger than 1MB and remove checksum attribute for params

* fix tool category in shed.yml

* formatting and another try to test location attribute

* add ftype

* review and correct preprocessing params, tests need to be added

* review and correct preprocessing params

* update preprocessing tests with new data

* add more tests for snap.tl functions

* Remove unnecessary functions and change tool naming

* remove macs3 and multiprocess dependencies

* remove ipynb

* read anndata into memory to overcome anndata metadata problem

* Use test data from Zenodo

* update the help text and fix the last test

* add two more dbscan clustering methods and fix njobs param

* add dbscan help

* some fixes and styles

* Update plotting.xml

* Update dimension_reduction_clustering.xml

* Update preprocessing.xml

---------

Co-authored-by: Pavankumar Videm <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>

tools/snapatac2/.shed.yml

@@ -0,0 +1,28 @@
+name: snapatac2
+owner: iuc
+description: "SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis"
+homepage_url: https://kzhang.org/SnapATAC2/
+long_description: |
+  SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework.
+
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2
+type: unrestricted
+categories:
+- Epigenetics
+- Sequence Analysis
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the snapatac2 tool suite: {{ tool_name }}"
+suite:
+  name: "suite_snapatac2"
+  description: "SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis"
+  long_description: |
+    SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring:
+
+      * Scale to more than 10 million cells.
+      * Blazingly fast preprocessing tools for BAM to fragment files conversion and count matrix generation.
+      * Matrix-free spectral embedding algorithm that is applicable to a wide range of single-cell omics data, including single-cell ATAC-seq, single-cell RNA-seq, single-cell Hi-C, and single-cell methylation.
+      * Efficient and scalable co-embedding algorithm for single-cell multi-omics data integration.
+      * End-to-end analysis pipeline for single-cell ATAC-seq data, including preprocessing, dimension reduction, clustering, data integration, peak calling, differential analysis, motif analysis, regulatory network analysis.
+      * Seamless integration with other single-cell analysis packages such as Scanpy.
+      * Implementation of fully backed AnnData.