# HG changeset patch
# User iuc
# Date 1651953359 0
# Node ID 9bd945a03d7bdacd13bd1d9b0acb36c190034f8a
# Parent  8db95f488f0f72d265ab52b36a9c1b14098e888e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"

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
@@ -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**
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
@@ -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.