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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d" |
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modified:
macros.xml manipulate.xml |
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| diff -r 8db95f488f0f -r 9bd945a03d7b macros.xml --- a/macros.xml Fri Feb 19 23:51:15 2021 +0000 +++ b/macros.xml Sat May 07 19:55:59 2022 +0000 |
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| @@ -46,7 +46,7 @@ and machine learning packages in Python (statsmodels, scikit-learn). More details on the `AnnData documentation -<https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__ +<https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.html>`__ **Loom data** |
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| diff -r 8db95f488f0f -r 9bd945a03d7b manipulate.xml --- a/manipulate.xml Fri Feb 19 23:51:15 2021 +0000 +++ b/manipulate.xml Sat May 07 19:55:59 2022 +0000 |
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| @@ -390,29 +390,29 @@ The possible manipulations are: -- Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) +- Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__) The `uns`, `varm` and `obsm` attributes are ignored. 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` -- 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>`__) +- 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>`__) The first occurance of a non-unique value is ignored. -- 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>`__) +- 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>`__) The first occurance of a non-unique value is ignored. -- Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) +- 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>`__) Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` -- Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) +- Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__) Only affects string annotations that lead to less categories than the total number of observations. -- Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__) +- Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__) Data matrix is transposed, observations and variables are interchanged. |