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Add Snapatac2 wrappers#5740

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bgruening merged 34 commits intogalaxyproject:maingalaxyproject/tools-iuc:mainfrom y4nnick8:snapatac2y4nnick8/tools-iuc:snapatac2Copy head branch name to clipboardMay 16, 2024

+1,603

Commits

Commits on Jan 29, 2024

• Add Snapatac2 wrappers

  y4nnick8

  committed
  593574c

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• add test data

  y4nnick8

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  837ed38

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Commits on Jan 31, 2024

• updated tools

  y4nnick8

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  d231a22

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Commits on Feb 1, 2024

• Merge branch 'galaxyproject:main' into snapatac2

  y4nnick8

  authored
  b76d68e

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Commits on Feb 4, 2024

• Fix some tests

  pavanvidem

  committed
  445aaff

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Commits on Feb 6, 2024

• Merge branch 'galaxyproject:main' into snapatac2

  y4nnick8

  authored
  2ff6e9b

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Commits on Feb 8, 2024

• update tools

  y4nnick8

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Commits on Feb 14, 2024

• update

  y4nnick8

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• added metrics.tsse to preprocessing.xml

  y4nnick8

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Commits on Feb 19, 2024

• tests tutorial1

  y4nnick8

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• added tl.umap test

  y4nnick8

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  ab0d586

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• fix tl.umap by setting NUMBA_CACHE_DIR variable

  pavanvidem

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Commits on Mar 1, 2024

• add .shed.yaml

  pavanvidem

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• add location for large files

  pavanvidem

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Commits on Mar 11, 2024

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

  pavanvidem

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Commits on Mar 20, 2024

• fix tool category in shed.yml

  pavanvidem

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Commits on Apr 4, 2024

• formatting and another try to test location attribute

  pavanvidem

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  ebcb83a

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• add ftype

  pavanvidem

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Commits on Apr 18, 2024

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

  pavanvidem

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  3679e43

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• review and correct preprocessing params

  pavanvidem

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Commits on Apr 29, 2024

• update preprocessing tests with new data

  pavanvidem

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Commits on May 13, 2024

• add more tests for snap.tl functions

  pavanvidem

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  44e050d

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Commits on May 14, 2024

• Remove unnecessary functions and change tool naming

  pavanvidem

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  652cda8

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• remove macs3 and multiprocess dependencies

  pavanvidem

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  08cc7e2

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• remove ipynb

  pavanvidem

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Commits on May 15, 2024

• read anndata into memory to overcome anndata metadata problem

  pavanvidem

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  2c42b52

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• Use test data from Zenodo

  pavanvidem

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  5aa8491

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• update the help text and fix the last test

  pavanvidem

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  4ef9ce8

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• add two more dbscan clustering methods and fix njobs param

  pavanvidem

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  3d8ef48

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• add dbscan help

  pavanvidem

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Commits on May 16, 2024

• some fixes and styles

  bgruening

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  40bd4e1

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• Update plotting.xml

  bgruening

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  c0c8b8b

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• Update dimension_reduction_clustering.xml

  bgruening

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• Update preprocessing.xml

  bgruening

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