| Previous changeset 13:6f83f8fd381f (2024-03-14) Next changeset 15:64ff3ef24fae (2024-07-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de |
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modified:
cluster_reduce_dimension.xml macros.xml |
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| diff -r 6f83f8fd381f -r 4d8f983cd751 cluster_reduce_dimension.xml --- a/cluster_reduce_dimension.xml Thu Mar 14 15:39:03 2024 +0000 +++ b/cluster_reduce_dimension.xml Sat May 18 18:28:35 2024 +0000 |
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| @@ -648,7 +648,7 @@ This requires to run `pp.neighbors`, first. More details on the `tl.louvain scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.louvain.html>`_ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.louvain.html>`_ Cluster cells into subgroups (`tl.leiden`) ========================================== @@ -658,7 +658,7 @@ The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015. More details on the `tl.leiden scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.leiden.html>`_ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.leiden.html>`_ Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca` ============================================================================================================ @@ -666,7 +666,7 @@ @CMD_pca_outputs@ More details on the `pp.pca scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.pca.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.pca.html>`__ Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca` ============================================================================================================ @@ -674,7 +674,7 @@ @CMD_pca_outputs@ More details on the `tl.pca scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.pca.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.pca.html>`__ Diffusion Maps, using `tl.diffmap` ================================== @@ -696,7 +696,7 @@ as colum. It can be accessed using the inspect tool for AnnData More details on the `tl.diffmap scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.diffmap.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.diffmap.html>`__ t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne` ======================================================================= @@ -708,7 +708,7 @@ It returns `X_tsne`, tSNE coordinates of data. More details on the `tl.tsne scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.tsne.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.tsne.html>`__ Embed the neighborhood graph using UMAP, using `tl.umap` ======================================================== @@ -728,7 +728,7 @@ observations annotation (obsm). This data is accessible using the inspect tool for AnnData More details on the `tl.umap scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.umap.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.umap.html>`__ Force-directed graph drawing, using `tl.draw_graph` =================================================== @@ -747,7 +747,7 @@ observations annotation (obsm). This data is accessible using the inspect tool for AnnData. More details on the `tl.draw_graph scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.draw_graph.html>`__ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.draw_graph.html>`__ Infer progression of cells through geodesic distance along the graph (`tl.dpt`) =============================================================================== @@ -776,7 +776,7 @@ The tool is similar to the R package `destiny` of Angerer et al (2016). More details on the `tl.dpt scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.dpt.html>`_ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.dpt.html>`_ Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`) @@ -807,7 +807,7 @@ These datasets are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects More details on the `tl.paga scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.paga.html>`_ +<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.paga.html>`_ ]]></help> <expand macro="citations"/> </tool> |
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| diff -r 6f83f8fd381f -r 4d8f983cd751 macros.xml --- a/macros.xml Thu Mar 14 15:39:03 2024 +0000 +++ b/macros.xml Sat May 18 18:28:35 2024 +0000 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.9.6</token> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@profile@">22.05</token> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@profile@">21.09</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> |