| Previous changeset 4:766be978777a (2019-12-18) Next changeset 6:77b91b9bdf52 (2020-02-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85" |
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modified:
cluster_reduce_dimension.xml |
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| diff -r 766be978777a -r 6f2d2c7f77ee cluster_reduce_dimension.xml --- a/cluster_reduce_dimension.xml Wed Dec 18 15:59:37 2019 -0500 +++ b/cluster_reduce_dimension.xml Mon Feb 10 05:27:02 2020 -0500 |
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| @@ -1,5 +1,5 @@ -<tool id="scanpy_cluster_reduce_dimension" name="Cluster," version="@galaxy_version@" profile="@profile@"> - <description>infer trajectories and embed with scanpy</description> +<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@galaxy_version@" profile="@profile@"> + <description>with scanpy</description> <macros> <import>macros.xml</import> <xml name="pca_inputs"> @@ -540,8 +540,8 @@ This requires to run `pp.neighbors`, first. -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.louvain.html>`_ +More details on the `tl.louvain scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.louvain.html>`_ Cluster cells into subgroups (`tl.leiden`) ========================================== @@ -550,24 +550,24 @@ The Louvain algorithm has been proposed for single-cell analysis by Levine et al, 2015. -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.leiden.html>`_ +More details on the `tl.leiden scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.leiden.html>`_ Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `pp.pca` ============================================================================================================ @CMD_pca_outputs@ -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.pca.html>`__ +More details on the `pp.pca scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.pca.html>`__ Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using `tl.pca` ============================================================================================================ @CMD_pca_outputs@ -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.pca.html>`__ +More details on the `tl.pca scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.pca.html>`__ Diffusion Maps, using `tl.diffmap` ================================== @@ -588,8 +588,8 @@ observations annotation (obsm). It is the right eigen basis of the transition matrix with eigenvectors as colum. It can be accessed using the inspect tool for AnnData -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.diffmap.html>`__ +More details on the `tl.diffmap scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.diffmap.html>`__ t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne` ======================================================================= @@ -600,8 +600,8 @@ It returns `X_tsne`, tSNE coordinates of data. -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.tsne.html>`__ +More details on the `tl.tsne scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.tsne.html>`__ Embed the neighborhood graph using UMAP, using `tl.umap` ======================================================== @@ -620,8 +620,8 @@ The UMAP coordinates of data are added to the return AnnData in the multi-dimensional observations annotation (obsm). This data is accessible using the inspect tool for AnnData -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.umap.html>`__ +More details on the `tl.umap scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.umap.html>`__ Force-directed graph drawing, using `tl.draw_graph` =================================================== @@ -639,8 +639,8 @@ The coordinates of graph layout are added to the return AnnData in the multi-dimensional observations annotation (obsm). This data is accessible using the inspect tool for AnnData. -More details on the `scanpy documentation -<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.draw_graph.html>`__ +More details on the `tl.draw_graph scanpy documentation +<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.draw_graph.html>`__ Infer progression of cells through geodesic distance along the graph (`tl.dpt`) =============================================================================== @@ -669,7 +669,7 @@ 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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.dpt.html>`_ Generate cellular maps of differentiation manifolds with complex topologies (`tl.paga`) @@ -700,7 +700,7 @@ 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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.paga.html>`_ ]]></help> <expand macro="citations"/> </tool> |