# HG changeset patch
# User iuc
# Date 1716056915 0
# Node ID 4d8f983cd7514d5a438e441a01ae3ac3e8c3da01
# Parent  6f83f8fd381fdfe3715f921e499a4c5e8a6ec935
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de

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
@@ -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>
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
@@ -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>