Mercurial > repos > iuc > anndata_manipulate

comparison manipulate.xml @ 10:4ebb4b3f1832 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
author iuc
date Sat, 07 May 2022 19:50:52 +0000
parents f1b4b1591958
children 9ac67979e25e
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9:89c8a68ee8e0 10:4ebb4b3f1832
388 388
389 This tool takes a AnnData dataset, manipulates it and returns it. 389 This tool takes a AnnData dataset, manipulates it and returns it.
390 390
391 The possible manipulations are: 391 The possible manipulations are:
392 392
393 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) 393 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__)
394 394
395 The `uns`, `varm` and `obsm` attributes are ignored. 395 The `uns`, `varm` and `obsm` attributes are ignored.
396 396
397 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN` 397 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`
398 398
399 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__) 399 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__)
400 400
401 The first occurance of a non-unique value is ignored. 401 The first occurance of a non-unique value is ignored.
402 402
403 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__) 403 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__)
404 404
405 The first occurance of a non-unique value is ignored. 405 The first occurance of a non-unique value is ignored.
406 406
407 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) 407 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__)
408 408
409 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` 409 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`
410 410
411 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) 411 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__)
412 412
413 Only affects string annotations that lead to less categories than the total number of observations. 413 Only affects string annotations that lead to less categories than the total number of observations.
414 414
415 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__) 415 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__)
416 416
417 Data matrix is transposed, observations and variables are interchanged. 417 Data matrix is transposed, observations and variables are interchanged.
418 418
419 - Add annotation for variables or observations 419 - Add annotation for variables or observations
420 420