# HG changeset patch
# User iuc
# Date 1726317946 0
# Node ID 178242b8229736b73ffda050438d0af1c0e06e62
# Parent  f9353ee6a0d4895b30599523d6290bf4ce168fdf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb

diff -r f9353ee6a0d4 -r 178242b82297 README.md
--- a/README.md	Tue Aug 20 09:50:17 2024 +0000
+++ b/README.md	Sat Sep 14 12:45:46 2024 +0000
@@ -25,6 +25,7 @@
     `pp.highly_variable_genes` | Extract highly variable genes
     `pp.subsample` | Subsample to a fraction of the number of observations
     `pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts
+    `pp.scrublet` | Predict doublets
 
 3. Normalize (`normalize.xml`)
 
@@ -34,14 +35,18 @@
     `pp.recipe_zheng17` | Normalization and filtering as of [Zheng17]
     `pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17]
     `pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15]
+    `external.pp.magic` | Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API
 
 4. Remove confounders (`remove_confounder.xml`)
 
     Methods | Description
     --- | ---
    `pp.regress_out` | Regress out unwanted sources of variation
-   `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors
+   <!-- `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors -->
    `pp.combat` | ComBat function for batch effect correction
+    `external.pp.bbknn` | Batch effect removal with Batch balanced KNN (BBKNN)
+    `external.pp.harmony_integrate` | Integrate multiple single-cell experiments with Harmony
+    `external.pp.scanorama_integrate` | Integrate multiple single-cell experiments with Scanorama
 
 5. Clustering, embedding and trajectory inference (`cluster_reduce_dimension.xml`)
 
@@ -49,14 +54,14 @@
     --- | ---
     `tl.louvain` | Cluster cells into subgroups
     `tl.leiden` | Cluster cells into subgroups
-    `tl.pca` | Principal component analysis
-    `pp.pca` | Principal component analysis (appears to be the same func...)
+    `pp.pca` | Principal component analysis
     `tl.diffmap` | Diffusion Maps
     `tl.tsne` | t-SNE
     `tl.umap` | Embed the neighborhood graph using UMAP
     `tl.draw_graph` | Force-directed graph drawing
     `tl.dpt` | Infer progression of cells through geodesic distance along the graph
     `tl.paga` | Mapping out the coarse-grained connectivity structures of complex manifolds
+    `tl.embedding_density` | Calculate the density of cells in an embedding (per condition)
 
 6. Plot (`plot.xml`)
 
@@ -66,18 +71,20 @@
         --- | ---
         `pl.scatter` | Scatter plot along observations or variables axes
         `pl.heatmap` | Heatmap of the expression values of set of genes
+        `pl.tracksplot` | Tracks plot of the expression values per cell
         `pl.dotplot` | Makes a dot plot of the expression values
         `pl.violin` | Violin plot
         `pl.stacked_violin` | Stacked violin plots
         `pl.matrixplot` | Heatmap of the mean expression values per cluster
         `pl.clustermap` | Hierarchically-clustered heatmap
-    
+
     2. Preprocessing
 
         Methods | Description
         --- | ---
         `pl.highest_expr_genes` | Plot the fraction of counts assigned to each gene over all cells
         `pl.highly_variable_genes` | Plot dispersions versus means for genes
+        `pl.scrublet_score_distribution` | Histogram of doublet scores
 
     3. PCA
 
@@ -96,12 +103,13 @@
         `pl.umap` | Scatter plot in UMAP basis
         `pl.diffmap` | Scatter plot in Diffusion Map basis
         `pl.draw_graph` | Scatter plot in graph-drawing basis
+        `pl.embedding_density` | Density of cells in an embedding (per condition)
 
     5. Branching trajectories and pseudotime, clustering
 
         Methods | Description
         --- | ---
-        `pl.dpt_groups_pseudotime` | Plot groups and pseudotime
+        <!-- `pl.dpt_groups_pseudotime` | Plot groups and pseudotime -->
         `pl.dpt_timeseries` | Heatmap of pseudotime series
         `pl.paga` | Plot the abstracted graph through thresholding low-connectivity edges
         `pl.paga_compare` | Scatter and PAGA graph side-by-side
@@ -113,3 +121,8 @@
         --- | ---
         `pl.rank_genes_groups` | Plot ranking of genes using dotplot plot
         `pl.rank_genes_groups_violin` | Plot ranking of genes for all tested comparisons
+        `pl.rank_genes_groups_stacked_violin` | Plot ranking of genes as stacked violin plot
+        `pl.rank_genes_groups_heatmap` | Plot ranking of genes as heatmap plot
+        `pl.rank_genes_groups_dotplot` | Plot ranking of genes as dotplot plot
+        `pl.rank_genes_groups_matrixplot` | Plot ranking of genes as matrixplot plot
+        `pl.rank_genes_groups_tracksplot` | Plot ranking of genes as tracksplot plot
diff -r f9353ee6a0d4 -r 178242b82297 cluster_reduce_dimension.xml
--- a/cluster_reduce_dimension.xml	Tue Aug 20 09:50:17 2024 +0000
+++ b/cluster_reduce_dimension.xml	Sat Sep 14 12:45:46 2024 +0000
@@ -1,37 +1,44 @@
-<tool id="scanpy_cluster_reduce_dimension" name="Cluster, infer trajectories and embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
-    <description>with scanpy</description>
+<tool id="scanpy_cluster_reduce_dimension" name="Scanpy cluster, embed" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>and infer trajectories</description>
     <macros>
         <import>macros.xml</import>
         <xml name="pca_inputs">
             <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help="If the value is larger than the number of observations the number of observations is used instead"/>
-            <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help="">
-                <expand macro="sanitize_query" />
+            <param argument="layer" type="text" value="" optional="true" label="If provided, which element of layers to use for PCA">
+                <expand macro="sanitize_query"/>
+            </param>
+            <param argument="dtype" type="select" label="Numpy data type string to which to convert the result">
+                <option value="float32" selected="true">float32</option>
+                <option value="int32">int32</option>
+                <option value="int64">int64</option>
+                <option value="uint32">uint32</option>
+                <option value="uint64">uint64</option>
+                <option value="float16">float16</option>
+                <option value="float64">float64</option>
             </param>
             <conditional name="pca">
                 <param argument="chunked" type="select" label="Type of PCA?">
+                    <option value="False" selected="true">Full PCA</option>
                     <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of 'random_seed' and 'svd_solver')</option>
-                    <option value="False" selected="true">Full PCA</option>
                 </param>
                 <when value="True">
                     <param argument="chunk_size" type="integer" min="0" value="" label="chunk_size" help="Number of observations to include in each chunk"/>
                 </when>
                 <when value="False">
-                    <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true"
-                        label="Compute standard PCA from covariance matrix?"
-                        help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>
+                    <param argument="zero_center" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Compute standard PCA from covariance matrix?" help="If not, it omits zero-centering variables (uses *TruncatedSVD* from scikit-learn), which allows to handle sparse input efficiently."/>
                     <expand macro="svd_solver"/>
-                    <param argument="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
+                    <param argument="random_state" type="integer" value="0" label="Change to use different initial states for the optimization"/>
                 </when>
             </conditional>
-            <param argument="use_highly_variable" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use highly variable genes only?" help="They should be use if they have been determined beforehand."/>
+            <param argument="mask_var" type="text" value="" optional="true" label="To run only on a certain set of genes given by a string referring to an array in" help="By default, uses .var['highly_variable'] if available, else everything"/>
         </xml>
         <xml name="param_random_state">
             <param argument="random_state" type="integer" value="0" label="Random state" help="Change the initialization of the optimization."/>
         </xml>
-        <xml name="param_use_weights">
-            <param argument="use_weights" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use weights from knn graph?"/>
+        <xml name="param_use_weights" token_checked="">
+            <param argument="use_weights" type="boolean" truevalue="True" falsevalue="False" checked="@CHECKED@" label="Use weights from knn graph?"/>
         </xml>
-        <token name="@CMD_pca_help@"><![CDATA[
+        <token name="@CMD_PCA_HELP@"><![CDATA[
 The PCA is computed using the implementation of *scikit-learn*.
 
 The returned AnnData object contains:
@@ -43,34 +50,25 @@
     - Explained variance, equivalent to the eigenvalues of the covariance matrix
 
 This data is accessible using the inspect tool for AnnData
-]]></token>
-        <token name="@CMD_pca_params@"><![CDATA[
-    data=adata,
-    n_comps=min($method.n_comps, adata.n_vars),
-    dtype='$method.dtype',
-    copy=False,
-    chunked=$method.pca.chunked,
-#if $method.pca.chunked == 'True'
-    chunk_size=$method.pca.chunk_size,
-#else
-    zero_center=$method.pca.zero_center,
-    svd_solver='$method.pca.svd_solver',
-    random_state=$method.pca.random_state,
-#end if
-    use_highly_variable=$method.use_highly_variable
-]]></token>
+        ]]>
+        </token>
     </macros>
     <expand macro="bio_tools"/>
     <expand macro="requirements">
+        <requirement type="package" version="0.5.6">umap-learn</requirement>
+        <requirement type="package" version="0.10.2">leidenalg</requirement>
+        <requirement type="package" version="0.8.2">louvain</requirement>
+        <requirement type="package" version="1.5.1">scikit-learn</requirement>
     </expand>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@
-      ]]></command>
+    ]]>
+    </command>
     <configfiles>
         <configfile name="script_file"><![CDATA[
-@CMD_imports@
-@CMD_read_inputs@
+@CMD_IMPORTS@
+@CMD_READ_INPUTS@
 
 #if $method.method == 'tl.louvain'
 sc.tl.louvain(
@@ -83,6 +81,7 @@
     key_added='$method.key_added',
     directed=$method.directed,
     use_weights=$method.use_weights,
+    @CMD_PARAM_NEIGHBORS_KEY@
     copy=False)
 
 #else if $method.method == 'tl.leiden'
@@ -91,33 +90,60 @@
     resolution=$method.resolution,
     random_state=$method.random_state,
     key_added='$method.key_added',
+    directed=$method.directed,
     use_weights=$method.use_weights,
     n_iterations=$method.n_iterations,
+    @CMD_PARAM_NEIGHBORS_KEY@
+    flavor='$method.flavor',
     copy=False)
 
 #else if $method.method == 'pp.pca'
-sc.pp.pca(@CMD_pca_params@)
-
-#else if $method.method == 'tl.pca'
-sc.tl.pca(@CMD_pca_params@)
+sc.pp.pca(
+    data=adata,
+    n_comps=min($method.n_comps, adata.n_vars-1),
+    #if $method.layer != ''
+    layer='$method.layer',
+    #end if
+    dtype='$method.dtype',
+    chunked=$method.pca.chunked,
+    #if $method.pca.chunked == 'True'
+    chunk_size=$method.pca.chunk_size,
+    #else
+    zero_center=$method.pca.zero_center,
+    #if $method.pca.svd_solver != ''
+    svd_solver='$method.pca.svd_solver',
+    #end if
+    random_state=$method.pca.random_state,
+    #end if
+    #if $method.mask_var != ''
+    mask_var='$method.mask_var',
+    #end if
+    copy=False)
 
 #else if $method.method == 'tl.diffmap'
 sc.tl.diffmap(
     adata=adata,
-    n_comps=min($method.n_comps, adata.n_vars),
+    n_comps=min($method.n_comps, adata.n_vars-1),
+    random_state=$method.random_state,
+    @CMD_PARAM_NEIGHBORS_KEY@
     copy =False)
 
 #else if $method.method == 'tl.tsne'
+import os
 sc.tl.tsne(
     adata=adata,
     #if str($method.n_pcs) != ''
     n_pcs=$method.n_pcs,
     #end if
+    #if $method.use_rep != ''
+    use_rep='$method.use_rep',
+    #end if
     perplexity=$method.perplexity,
+    metric='$method.metric',
     early_exaggeration=$method.early_exaggeration,
     learning_rate=$method.learning_rate,
     random_state=$method.random_state,
-    use_fast_tsne=$method.use_fast_tsne,
+    n_jobs = int(os.getenv("GALAXY_SLOTS", 4)),
     copy=False)
 
 #else if $method.method == 'tl.umap'
@@ -134,6 +160,7 @@
     negative_sample_rate=$method.negative_sample_rate,
     init_pos='$method.init_pos',
     random_state=$method.random_state,
+    @CMD_PARAM_NEIGHBORS_KEY@
     copy=False)
 
 #else if $method.method == 'tl.draw_graph'
@@ -145,28 +172,20 @@
 sc.tl.draw_graph(
     adata=adata,
     layout='$method.layout',
-#if $method.root
-    #set $root=([int(x.strip()) for x in str($method.root).split(',')])
-    root=$root,
-#end if
+    #if str($method.root)
+    root=$method.root,
+    #end if
     random_state=$method.random_state,
-    #if $method.init_pos
-    init_pos='$method.init_pos',
-    #end if
     #if str($method.adjacency) != 'None'
     adjacency=adjacency,
     #end if
-    #if $method.key_ext
-    key_ext='$method.key_ext',
+    #if $method.key_added_ext != ''
+    key_added_ext='$method.key_added_ext',
     #end if
-    copy=False)
-
-#else if $method.method == "tl.paga"
-sc.tl.paga(
-    adata=adata,
-    groups='$method.groups',
-    use_rna_velocity=$method.use_rna_velocity,
-    model='$method.model',
+    #if $method.init_pos != ''
+    init_pos='$method.init_pos',
+    #end if
+    @CMD_PARAM_NEIGHBORS_KEY@
     copy=False)
 
 #else if $method.method == "tl.dpt"
@@ -176,24 +195,37 @@
     n_branchings=$method.n_branchings,
     min_group_size=$method.min_group_size,
     allow_kendall_tau_shift=$method.allow_kendall_tau_shift,
+    @CMD_PARAM_NEIGHBORS_KEY@
+    copy=False)
+
+#else if $method.method == "tl.paga"
+sc.tl.paga(
+    adata=adata,
+    #if $method.groups != '':
+    groups='$method.groups',
+    #end if
+    use_rna_velocity=$method.use_rna_velocity,
+    model='$method.model',
+    @CMD_PARAM_NEIGHBORS_KEY@
     copy=False)
 
 #else if $method.method == "tl.embedding_density"
 sc.tl.embedding_density(
     adata=adata,
     basis='$method.basis',
-#if $method.groupby
+    #if $method.groupby != ''
     groupby='$method.groupby',
-#end if
-#if $method.key_added
+    #end if
+    #if $method.key_added != ''
     key_added='$method.key_added',
-#end if
+    #end if
     )
 
 #end if
 
-@CMD_anndata_write_outputs@
-]]></configfile>
+@CMD_ANNDATA_WRITE_OUTPUTS@
+        ]]>     
+        </configfile>
     </configfiles>
     <inputs>
         <expand macro="inputs_anndata"/>
@@ -202,113 +234,123 @@
                 <option value="tl.louvain">Cluster cells into subgroups, using 'tl.louvain'</option>
                 <option value="tl.leiden">Cluster cells into subgroups, using 'tl.leiden'</option>
                 <option value="pp.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using 'pp.pca'</option>
-                <option value="tl.pca">Computes PCA (principal component analysis) coordinates, loadings and variance decomposition, using 'tl.pca'</option>
                 <option value="tl.diffmap">Diffusion Maps, using 'tl.diffmap'</option>
                 <option value="tl.tsne">t-distributed stochastic neighborhood embedding (tSNE), using 'tl.tsne'</option>
                 <option value="tl.umap">Embed the neighborhood graph using UMAP, using 'tl.umap'</option>
                 <option value="tl.draw_graph">Force-directed graph drawing, using 'tl.draw_graph'</option>
                 <option value="tl.dpt">Infer progression of cells through geodesic distance along the graph, using 'tl.dpt'</option>
                 <option value="tl.paga">Generate cellular maps of differentiation manifolds with complex topologies, using 'tl.paga'</option>
-                <option value="tl.embedding_density">Calculate the density of cells in an embedding (per condition)</option>
+                <option value="tl.embedding_density">Calculate the density of cells in an embedding (per condition), using 'tl.embedding_density'</option>
             </param>
             <when value="tl.louvain">
                 <conditional name="flavor">
-                    <param argument="flavor" type="select" label="Flavor for the clustering" help="">
-                        <option value="vtraag">vtraag (much more powerful)</option>
-                        <option value="igraph">igraph</option>
+                    <param argument="flavor" type="select" label="Flavor for the clustering">
+                        <option value="vtraag" selected="true">vtraag (much more powerful than igraph)</option>
+                        <option value="igraph">Built in igraph method</option>
                     </param>
                     <when value="vtraag">
-                        <param argument="resolution" type="float" value="1.0"
-                            label="Resolution"
-                            help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2009"/>
+                        <param argument="resolution" type="float" value="1.0" label="Resolution" help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2014"/>
                     </when>
                     <when value="igraph"/>
                 </conditional>
                 <expand macro="param_random_state"/>
-                <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help="">
-                    <expand macro="sanitize_query" />
+                <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels">
+                    <expand macro="sanitize_query"/>
                 </param>
                 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/>
-                <expand macro="param_use_weights"/>
+                <expand macro="param_use_weights" checked="false"/>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.leiden">
                 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/>
                 <expand macro="param_random_state"/>
-                <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help="">
-                    <expand macro="sanitize_query" />
+                <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels">
+                    <expand macro="sanitize_query"/>
                 </param>
-                <expand macro="param_use_weights"/>
+                <param argument="directed" type="boolean" truevalue="True" falsevalue="None" checked="false" label="Treat the graph as directed or undirected?"/>
+                <expand macro="param_use_weights" checked="true"/>
                 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
+                <expand macro="param_neighbors_key"/>
+                <param argument="flavor" type="select" label="Flavor for the clustering">
+                    <option value="leidenalg" selected="true">leidenalg</option>
+                    <option value="igraph">Built in igraph method</option>
+                </param>
             </when>
             <when value="pp.pca">
                 <expand macro="pca_inputs"/>
             </when>
-            <when value="tl.pca">
-                <expand macro="pca_inputs"/>
-            </when>
             <when value="tl.diffmap">
-                <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation" help=""/>
+                <param argument="n_comps" type="integer" min="0" value="15" optional="true" label="Number of dimensions of the representation"/>
+                <param argument="random_state" type="integer" value="0" label="Seed used by the random number generator"/>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.tsne">
-                <param name="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
-                <param name="perplexity" type="float" value="30" label="Perplexity" help="The perplexity is related to the number of nearest neighbors that is used in other manifold learning algorithms. Larger datasets usually require a larger perplexity. Consider selecting a value between 5 and 50. The choice is not extremely critical since t-SNE is quite insensitive to this parameter."/>
-                <param name="early_exaggeration" type="float" value="12.0" label="Early exaggeration" help="Controls how tight natural clusters in the original space are in the embedded space and how much space will be between them. For larger values, the space between natural clusters will be larger in the embedded space. Again, the choice of this parameter is not very critical. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high."/>
-                <param name="learning_rate" type="float" value="1000" label="Learning rate" help="The learning rate can be a critical parameter. It should be between 100 and 1000. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high. If the cost function gets stuck in a bad local minimum increasing the learning rate helps sometimes."/>
-                <param name="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
-                <param argument="use_fast_tsne" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use the MulticoreTSNE package if possible?"/>
+                <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use"/>
+                <expand macro="param_use_rep"/>
+                <param argument="perplexity" type="float" value="30" label="Perplexity" help="The perplexity is related to the number of nearest neighbors that is used in other manifold learning algorithms. Larger datasets usually require a larger perplexity. Consider selecting a value between 5 and 50. The choice is not extremely critical since t-SNE is quite insensitive to this parameter."/>
+                <param argument="metric" type="select">
+                    <expand macro="distance_metric_options"/>
+                </param>
+                <param argument="early_exaggeration" type="float" value="12.0" label="Early exaggeration" help="Controls how tight natural clusters in the original space are in the embedded space and how much space will be between them. For larger values, the space between natural clusters will be larger in the embedded space. Again, the choice of this parameter is not very critical. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high."/>
+                <param argument="learning_rate" type="float" value="1000" label="Learning rate" help="The learning rate can be a critical parameter. It should be between 100 and 1000. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high. If the cost function gets stuck in a bad local minimum increasing the learning rate helps sometimes."/>
+                <param argument="random_state" type="integer" value="0" label="Random state" help="Change this to use different intial states for the optimization"/>
             </when>
             <when value="tl.umap">
                 <param argument="min_dist" type="float" value="0.5" label="Effective minimum distance between embedded points" help="Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the 'spread' value, which determines the scale at which embedded points will be spread out. The default of in the 'umap-learn' package is 0.1."/>
                 <param argument="spread" type="float" value="1.0" label="Effective scale of embedded points" help="In combination with 'min_dist' this determines how clustered/clumped the embedded points are."/>
-                <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding" help=""/>
+                <param argument="n_components" type="integer" min="0" value="2" label="Number of dimensions of the embedding"/>
                 <param argument="maxiter" type="integer" min="0" value="" optional="true" label="Number of iterations (epochs) of the optimization" help="Called 'n_epochs' in the original UMAP."/>
-                <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization" help=""/>
+                <param argument="alpha" type="float" value="1.0" label="Initial learning rate for the embedding optimization"/>
                 <param argument="gamma" type="float" value="1.0" label="Weighting applied to negative samples in low dimensional embedding optimization" help="Values higher than one will result in greater weight being given to negative samples."/>
-                <param argument="negative_sample_rate" type="integer" min="0" value="5" label="The number of negative edge/1-simplex samples to use per positive edge/1-simplex sample in optimizing the low dimensional embedding" help=""/>
+                <param argument="negative_sample_rate" type="integer" min="0" value="5" label="The number of negative edge/1-simplex samples to use per positive edge/1-simplex sample in optimizing the low dimensional embedding"/>
                 <param argument="init_pos" type="select" label="How to initialize the low dimensional embedding" help="Called 'init' in the original UMAP">
+                    <option value="spectral" selected="true">Spectral embedding of the graph</option>
                     <option value="paga">Position from paga</option>
-                    <option value="spectral" selected="true">Spectral embedding of the graph</option>
                     <option value="random">Initial embedding positions at random</option>
                 </param>
-                <expand macro="param_random_state"/>
+                <param argument="random_state" type="integer" value="0" label="Seed used by the random number generator"/>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.draw_graph">
                 <expand macro="param_layout"/>
-                <expand macro="param_root"/>
-                <expand macro="param_random_state"/>
-                <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)">
-                    <expand macro="sanitize_query" />
+                <param argument="root" type="integer" value="" optional="true" label="Root for tree layouts"/>
+                <param argument="random_state" type="integer" value="0" optional="true" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization."/>
+                <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/>
+                <param argument="key_added_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'">
+                    <expand macro="sanitize_query"/>
                 </param>
-                <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/>
-                <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'">
-                    <expand macro="sanitize_query" />
+                <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)">
+                    <expand macro="sanitize_query"/>
                 </param>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.dpt">
-                <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/>
-                <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect" help=""/>
+                <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use"/>
+                <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect"/>
                 <param argument="min_group_size" type="float" min="0" value="0.01" label="Min group size" help="During recursive splitting of branches ('dpt groups') for 'n_branchings' &gt; 1, do not consider groups that contain less than 'min_group_size' data points. If a float, 'min_group_size' refers to a fraction of the total number of data points."/>
                 <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.paga">
-                <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs').">
-                    <expand macro="sanitize_query" />
+                <param argument="groups" type="text" optional="true" value="" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs').">
+                    <expand macro="sanitize_query"/>
                 </param>
                 <param argument="use_rna_velocity" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/>
-                <param argument="model" type="select" label="PAGA connectivity model" help="">
-                    <option value="v1.2">v1.2</option>
+                <param argument="model" type="select" label="PAGA connectivity model">
+                    <option value="v1.2" selected="true">v1.2</option>
                     <option value="v1.0">v1.0</option>
                 </param>
+                <expand macro="param_neighbors_key"/>
             </when>
             <when value="tl.embedding_density">
                 <param argument="basis" type="text" value="umap" label="The embedding over which the density will be calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
-                    <expand macro="sanitize_query" />
+                    <expand macro="sanitize_query"/>
                 </param>
                 <param argument="groupby" type="text" optional="true" value="" label="Key for categorical observation/cell annotation for which densities are calculated per category." >
-                    <expand macro="sanitize_query" />
+                    <expand macro="sanitize_query"/>
                 </param>
                 <param argument="key_added" type="text" optional="true" value="" label="Name of the .obs covariate that will be added with the density estimates.">
-                    <expand macro="sanitize_query" />
+                    <expand macro="sanitize_query"/>
                 </param>
             </when>
         </conditional>
@@ -318,22 +360,16 @@
         <expand macro="anndata_outputs"/>
     </outputs>
     <tests>
+
+        <!-- test 1 -->
         <test expect_num_outputs="2">
-            <!-- test 1 -->
-            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
+            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.louvain"/>
-                <conditional name="flavor">
-                    <param name="flavor" value="vtraag"/>
-                    <param name="resolution" value="1.0"/>
-                </conditional>
                 <param name="random_state" value="10"/>
-                <param name="key_added" value="louvain"/>
-                <param name="directed" value="true"/>
-                <param name="use_weights" value="false"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -347,21 +383,23 @@
                     <has_text_matching expression="use_weights=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/louvain"/>
+                    <has_h5_keys keys="uns/louvain"/>
+                </assert_contents>
+            </output>
         </test>
+
+        <!-- test 2 -->
         <test expect_num_outputs="2">
-            <!-- test 2 -->
-            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
+            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.leiden"/>
-                <param name="random_state" value="1"/>
                 <param name="random_state" value="10"/>
-                <param name="key_added" value="leiden"/>
-                <param name="use_weights" value="false"/>
-                <param name="n_iterations" value="-1"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -369,29 +407,26 @@
                     <has_text_matching expression="resolution=1"/>
                     <has_text_matching expression="random_state=10"/>
                     <has_text_matching expression="key_added='leiden'"/>
-                    <has_text_matching expression="use_weights=False"/>
+                    <has_text_matching expression="use_weights=True"/>
                     <has_text_matching expression="n_iterations=-1"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/leiden"/>
+                    <has_h5_keys keys="uns/leiden"/>
+                </assert_contents>
+            </output>
         </test>
+
+        <!-- test 3 -->
         <test expect_num_outputs="2">
-            <!-- test 3 -->
-            <param name="adata" value="krumsiek11.h5ad" />
+            <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
                 <param name="method" value="pp.pca"/>
-                <param name="n_comps" value="50"/>
-                <param name="dtype" value="float32"/>
-                <conditional name="pca">
-                    <param name="chunked" value="False"/>
-                    <param name="zero_center" value="true"/>
-                    <param name="svd_solver" value="auto"/>
-                    <param name="random_state" value="0"/>
-                </conditional>
-                <param name="use_highly_variable" value="false"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -400,28 +435,31 @@
                     <has_text_matching expression="copy=False"/>
                     <has_text_matching expression="chunked=False"/>
                     <has_text_matching expression="zero_center=True"/>
-                    <has_text_matching expression="svd_solver='auto'"/>
                     <has_text_matching expression="random_state=0"/>
-                    <has_text_matching expression="use_highly_variable=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/pca"/>
+                    <has_h5_keys keys="obsm/X_pca"/>
+                    <has_h5_keys keys="varm/PCs"/>
+                </assert_contents>
+            </output>
         </test>
+
+        <!-- test 4 -->
         <test expect_num_outputs="2">
-            <!-- test 4 -->
-            <param name="adata" value="krumsiek11.h5ad" />
+            <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
                 <param name="method" value="pp.pca"/>
                 <param name="n_comps" value="20"/>
-                <param name="dtype" value="float32"/>
                 <conditional name="pca">
                     <param name="chunked" value="True"/>
                     <param name="chunk_size" value="50"/>
                 </conditional>
-                <param name="use_highly_variable" value="false"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -431,73 +469,48 @@
                     <has_text_matching expression="copy=False"/>
                     <has_text_matching expression="chunked=True"/>
                     <has_text_matching expression="chunk_size=50"/>
-                    <has_text_matching expression="use_highly_variable=False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/pca"/>
+                    <has_h5_keys keys="obsm/X_pca"/>
+                    <has_h5_keys keys="varm/PCs"/>
+                </assert_contents>
+            </output>
         </test>
+        
+        <!-- test 5 -->
         <test expect_num_outputs="2">
-            <!-- test 5 -->
-            <param name="adata" value="krumsiek11.h5ad" />
+            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
-                <param name="method" value="tl.pca"/>
-                <param name="n_comps" value="50"/>
-                <param name="dtype" value="float32"/>
-                <conditional name="pca">
-                    <param name="chunked" value="False"/>
-                    <param name="zero_center" value="True"/>
-                    <param name="svd_solver" value="auto"/>
-                    <param name="random_state" value="0"/>
-                </conditional>
-                <param name="use_highly_variable" value="false"/>
+                <param name="method" value="tl.diffmap"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
-            </section>
-            <output name="hidden_output">
-                <assert_contents>
-                    <has_text_matching expression="sc.tl.pca"/>
-                    <has_text_matching expression="dtype='float32'"/>
-                    <has_text_matching expression="copy=False"/>
-                    <has_text_matching expression="chunked=False"/>
-                    <has_text_matching expression="zero_center=True"/>
-                    <has_text_matching expression="svd_solver='auto'"/>
-                    <has_text_matching expression="use_highly_variable=False"/>
-                </assert_contents>
-            </output>
-            <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.15"/>
-        </test>
-        <test expect_num_outputs="2">
-            <!-- test 6 -->
-            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
-            <conditional name="method">
-                <param name="method" value="tl.diffmap"/>
-                <param name="n_comps" value="15"/>
-            </conditional>
-            <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
                     <has_text_matching expression="sc.tl.diffmap"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obsm/X_diffmap"/>
+                    <has_h5_keys keys="uns/diffmap_evals"/>
+                </assert_contents>
+            </output>
         </test>
+        
+        <!-- test 6 -->
         <test expect_num_outputs="2">
-            <!-- test 7 -->
-            <param name="adata" value="krumsiek11.h5ad" />
+            <param name="adata" value="krumsiek11.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.tsne"/>
                 <param name="n_pcs" value="10"/>
-                <param name="perplexity" value="30"/>
-                <param name="early_exaggeration" value="12.0"/>
-                <param name="learning_rate" value="1000"/>
-                <param name="random_state" value="0"/>
-                <param name="use_fast_tsne" value="true"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -507,28 +520,25 @@
                     <has_text_matching expression="early_exaggeration=12.0"/>
                     <has_text_matching expression="learning_rate=1000.0"/>
                     <has_text_matching expression="random_state=0"/>
-                    <has_text_matching expression="use_fast_tsne=True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/tsne"/>
+                    <has_h5_keys keys="obsm/X_tsne"/>
+                </assert_contents>
+            </output>
         </test>
+        
+        <!-- test 7 -->
         <test expect_num_outputs="2">
-            <!-- test 8 -->
-            <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
+            <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.umap"/>
-                <param name="min_dist" value="0.5"/>
-                <param name="spread" value="1.0"/>
-                <param name="n_components" value="2"/>
                 <param name="maxiter" value="2"/>
-                <param name="alpha" value="1.0"/>
-                <param name="gamma" value="1.0"/>
-                <param name="negative_sample_rate" value="5"/>
-                <param name="init_pos" value="spectral"/>
-                <param name="random_state" value="0"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -544,22 +554,22 @@
                     <has_text_matching expression="random_state=0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
+            <output name="anndata_out" ftype="h5ad">
                 <assert_contents>
-                    <has_h5_keys keys="X, obs, obsm, uns, var" />
+                    <has_h5_keys keys="uns/umap"/>
+                    <has_h5_keys keys="obsm/X_umap"/>
                 </assert_contents>
             </output>
         </test>
+
+        <!-- test 8 -->
         <test expect_num_outputs="2">
-            <!-- test 9 -->
             <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.draw_graph"/>
-                <param name="layout" value="fa"/>
-                <param name="random_state" value="0"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -568,42 +578,24 @@
                     <has_text_matching expression="random_state=0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
-        </test>
-        <test expect_num_outputs="2">
-            <!-- test 10 -->
-            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
-            <conditional name="method">
-                <param name="method" value="tl.paga"/>
-                <param name="groups" value="paul15_clusters"/>
-                <param name="use_rna_velocity" value="False"/>
-                <param name="model" value="v1.2"/>
-            </conditional>
-            <section name="advanced_common">
-                <param name="show_log" value="true" />
-            </section>
-            <output name="hidden_output">
+            <output name="anndata_out" ftype="h5ad">
                 <assert_contents>
-                    <has_text_matching expression="sc.tl.paga"/>
-                    <has_text_matching expression="groups='paul15_clusters'"/>
-                    <has_text_matching expression="use_rna_velocity=False"/>
-                    <has_text_matching expression="model='v1.2'"/>
+                    <has_h5_keys keys="uns/draw_graph"/>
+                    <has_h5_keys keys="obsm/X_draw_graph_fr"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
         </test>
+
+        <!-- test 9 -->
         <test expect_num_outputs="2">
-            <!-- test 11 -->
-            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
+            <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.dpt"/>
                 <param name="n_dcs" value="15"/>
                 <param name="n_branchings" value="1"/>
-                <param name="min_group_size" value="0.01"/>
-                <param name="allow_kendall_tau_shift" value="True"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -614,18 +606,48 @@
                     <has_text_matching expression="allow_kendall_tau_shift=True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/dpt_groups,obs/dpt_order,obs/dpt_order_indices"/>
+                    <has_h5_keys keys="uns/dpt_changepoints,uns/dpt_grouptips"/>
+                </assert_contents>
+            </output>
         </test>
+
+        <!-- test 10 -->
+        <test expect_num_outputs="2">    
+            <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
+            <conditional name="method">
+                <param name="method" value="tl.paga"/>
+                <param name="groups" value="paul15_clusters"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sc.tl.paga"/>
+                    <has_text_matching expression="groups='paul15_clusters'"/>
+                    <has_text_matching expression="use_rna_velocity=False"/>
+                    <has_text_matching expression="model='v1.2'"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="uns/paga,uns/paul15_clusters_sizes"/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <!-- test 11 -->
         <test expect_num_outputs="2">
-            <!-- test 12 -->
-            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
+            <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
             <conditional name="method">
                 <param name="method" value="tl.embedding_density"/>
-                <param name="basis" value="umap"/>
                 <param name="key_added" value="umap_density"/>
             </conditional>
             <section name="advanced_common">
-                <param name="show_log" value="true" />
+                <param name="show_log" value="true"/>
             </section>
             <output name="hidden_output">
                 <assert_contents>
@@ -634,10 +656,16 @@
                     <has_text_matching expression="key_added='umap_density'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" file="tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
+            <output name="anndata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="obs/umap_density"/>
+                    <has_h5_keys keys="uns/umap_density_params"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
+        
 Cluster cells into subgroups (`tl.louvain`)
 ===========================================
 
@@ -650,6 +678,7 @@
 More details on the `tl.louvain scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.louvain.html>`_
 
+
 Cluster cells into subgroups (`tl.leiden`)
 ==========================================
 
@@ -660,21 +689,13 @@
 More details on the `tl.leiden scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/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 `pp.pca scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/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 `tl.pca scanpy documentation
-<https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.pca.html>`__
 
 Diffusion Maps, using `tl.diffmap`
 ==================================
@@ -698,6 +719,7 @@
 More details on the `tl.diffmap scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.diffmap.html>`__
 
+
 t-distributed stochastic neighborhood embedding (tSNE), using `tl.tsne`
 =======================================================================
 
@@ -710,6 +732,7 @@
 More details on the `tl.tsne scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.tsne.html>`__
 
+
 Embed the neighborhood graph using UMAP, using `tl.umap`
 ========================================================
 
@@ -721,8 +744,8 @@
 nearest-neighbor distances in the embedding such that these best match the
 distribution of distances in the high-dimensional space.  We use the
 implementation of `umap-learn <https://github.com/lmcinnes/umap>`__
-(McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `preprint
-<https://doi.org/10.1101/298430>`__.
+(McInnes et al, 2018). For a few comparisons of UMAP with tSNE, see this `paper
+<https://www.nature.com/articles/nbt.4314>`__.
 
 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
@@ -730,6 +753,7 @@
 More details on the `tl.umap scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.umap.html>`__
 
+
 Force-directed graph drawing, using `tl.draw_graph`
 ===================================================
 
@@ -749,6 +773,7 @@
 More details on the `tl.draw_graph scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.draw_graph.html>`__
 
+
 Infer progression of cells through geodesic distance along the graph (`tl.dpt`)
 ===============================================================================
 
@@ -808,6 +833,18 @@
 
 More details on the `tl.paga scanpy documentation
 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.paga.html>`_
-    ]]></help>
+
+
+Calculates the density of cells in an embedding (per condition). (`tl.embedding_density`)
+=========================================================================================
+
+Gaussian kernel density estimation is used to calculate the density of cells in an embedded space. This can be performed per category over a categorical cell annotation.
+
+Note that density values are scaled to be between 0 and 1. Thus, the density value at each cell is only comparable to densities in the same category.
+
+More details on the `tl.embedding_density scanpy documentation
+<https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.embedding_density.html>`_
+    ]]>
+    </help>
     <expand macro="citations"/>
 </tool>
diff -r f9353ee6a0d4 -r 178242b82297 macros.xml
--- a/macros.xml	Tue Aug 20 09:50:17 2024 +0000
+++ b/macros.xml	Sat Sep 14 12:45:46 2024 +0000
@@ -1,17 +1,15 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.9.6</token>
-    <token name="@VERSION_SUFFIX@">4</token>
-    <token name="@profile@">21.09</token>
+    <token name="@TOOL_VERSION@">1.10.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
-            <requirement type="package" version="3.0.6">loompy</requirement>
-            <requirement type="package" version="0.10.1">leidenalg</requirement>
-            <requirement type="package" version="0.8.1">louvain</requirement>
-            <requirement type="package" version="1.5.3">pandas</requirement>
-            <requirement type="package" version="3.7">matplotlib</requirement>
-            <requirement type="package" version="0.12.2">seaborn</requirement>
-            <requirement type="package" version="3.0.0">magic-impute</requirement>
+            <requirement type="package" version="0.10.3">anndata</requirement>
+            <requirement type="package" version="1.26.4">numpy</requirement>
+            <requirement type="package" version="2.2.2">pandas</requirement>
+            <requirement type="package" version="1.14.1">scipy</requirement>
+            <requirement type="package" version="0.14.2">statsmodels</requirement>           
             <yield />
         </requirements>
     </xml>
@@ -22,7 +20,7 @@
     </xml>
     <xml name="creators">
         <creator>
-            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/"/>
         </creator>
     </xml>
     <xml name="citations">
@@ -31,28 +29,13 @@
             <citation type="doi">10.1093/gigascience/giaa102</citation>
         </citations>
     </xml>
-    <xml name="version_command">
-        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
-    </xml>
-    <token name="@CMD@"><![CDATA[
-cp '$adata' 'anndata.h5ad' &&
-cat '$script_file' > '$hidden_output' &&
-python '$script_file' >> '$hidden_output' &&
-ls . >> '$hidden_output' &&
-touch 'anndata_info.txt' &&
-cat 'anndata_info.txt' @CMD_prettify_stdout@
-    ]]>
-    </token>
-    <token name="@CMD_imports@"><![CDATA[
-import scanpy as sc
-import pandas as pd
-import numpy as np
-    ]]>
-    </token>
+    
+    
+    <!-- param macros -->
     <xml name="sanitize_query" token_validinitial="string.printable">
         <sanitizer>
             <valid initial="@VALIDINITIAL@">
-                <remove value="&apos;" />
+                <remove value="&apos;"/>
             </valid>
        </sanitizer>
     </xml>
@@ -62,58 +45,55 @@
                 <add value=","/>
             </valid>
         </sanitizer>
-    </xml>
+    </xml>      
     <xml name="inputs_anndata">
         <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
     </xml>
-    <token name="@CMD_read_inputs@"><![CDATA[
-adata = sc.read_h5ad('anndata.h5ad')
-]]>
-    </token>
     <xml name="inputs_common_advanced">
         <section name="advanced_common" title="Advanced Options" expanded="false">
-            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+            <param name="show_log" type="boolean" checked="false" label="Output Log?"/>
         </section>
     </xml>
     <xml name="anndata_outputs">
-        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
-            <data name="hidden_output" format="txt" label="Log file" >
+        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
+            <yield />
+        </data>
+        <data name="hidden_output" format="txt" label="Log file" >
             <filter>advanced_common['show_log']</filter>
         </data>
+    </xml>    
+    <xml name="param_use_rep">
+        <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
+                <expand macro="sanitize_query"/>
+        </param>
     </xml>
-    <token name="@CMD_anndata_write_outputs@"><![CDATA[
-adata.write_h5ad('anndata.h5ad')
-with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
-    print(adata, file=ainfo)
-]]>
-    </token>
-    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
-    ]]></token>
     <xml name="svd_solver">
-        <param name="svd_solver" type="select" label="SVD solver to use" help="">
+        <param name="svd_solver" type="select" optional="true" label="SVD solver to use">
             <option value="auto">Automatically chosen depending on the size of the problem</option>
             <option value="arpack">ARPACK wrapper in SciPy</option>
             <option value="randomized">Randomized algorithm due to Halko (2009)</option>
+            <option value="lobpcg">An alternative SciPy solver. Not available with dask arrays.</option>
+            <option value="tsqr">Only available with dask arrays. “tsqr” algorithm from Benson et. al. (2013).</option>
         </param>
     </xml>
     <xml name="pca_random_state">
-        <param name="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
+        <param name="random_state" type="integer" value="0" label="Initial states for the optimization"/>
     </xml>
     <xml name="param_plot_format">
         <param name="format" type="select" label="Format for saving figures">
-            <option value="png">png</option>
+            <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
             <option value="svg">svg</option>
         </param>
     </xml>
     <xml name="numeric_distance_metric_options">
+    	<option value="euclidean" selected="true">euclidean</option>
         <option value="braycurtis">braycurtis</option>
         <option value="canberra">canberra</option>
         <option value="chebyshev">chebyshev</option>
         <option value="cityblock">cityblock</option>
         <option value="correlation">correlation</option>
         <option value="cosine">cosine</option>
-        <option value="euclidean" selected="true">euclidean</option>
         <option value="mahalanobis">mahalanobis</option>
         <option value="matching">matching</option>
         <option value="minkowski">minkowski</option>
@@ -393,141 +373,6 @@
         <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option>
         <option value="gist_ncar">gist_ncar (Miscellaneous)</option>
     </xml>
-    <xml name="param_groupby">
-        <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into 'num_categories'.">
-            <expand macro="sanitize_query" />
-        </param>
-    </xml>
-    <xml name="param_use_raw">
-        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/>
-    </xml>
-    <xml name="param_log">
-        <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>
-    </xml>
-    <xml name="pl_figsize">
-        <conditional name="figsize">
-            <param name="test" type="select" label="Custom figure size" >
-                <option value="yes">Yes</option>
-                <option value="no" selected="true">No: the figure width is set based on the number of variable names and the height is set to 10.</option>
-            </param>
-            <when value="yes">
-                <param argument="width" type="integer" min="0" value="10" label="Figure width" help=""/>
-                <param argument="height" type="integer" min="0" value="10" label="Figure height" help=""/>
-            </when>
-            <when value="no"/>
-        </conditional>
-    </xml>
-    <token name="@CMD_params_figsize@"><![CDATA[
-
-    ]]></token>
-    <xml name="pl_var_names">
-        <conditional name="var_names">
-            <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
-                <option value="all">All variables in 'adata.var_names'</option>
-                <option value="custom">Subset of variables in 'adata.var_names'</option>
-                <option value="customfile">Subset of variables as a tabular file</option>
-            </param>
-            <when value="all"/>
-            <when value="custom">
-                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma">
-                    <expand macro="sanitize_query" />
-                </param>
-            </when>
-            <when value="customfile">
-                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
-                <param name="header" type="select" label="Header in the list of markers?">
-                    <option value="included">Header incldued</option>
-                    <option value="not_included">Header not included</option>
-                </param>
-            </when>
-        </conditional>
-    </xml>
-    <xml name="param_num_categories">
-        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>
-    </xml>
-    <xml name="param_dendrogram">
-        <param argument="dendrogram" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Compute and plot a dendrogram?" help="groupby categories are reordered accoring to the dendrogram order. If groups of var_names are set and those groups correspond to the groupby categories, those groups are also reordered. The ‘person’ method is used to compute the pairwise correlation between categories using all var_names in raw if use_raw is None, otherwise all adata.var_names are used. The linkage method used is complete."/>
-    </xml>
-    <xml name="pl_var_group_positions">
-        <repeat name="var_group_positions" title="Group of variables to highlight" help="This will draw a 'bracket' on top of the plot between the given start and end positions. If a label is given, it will be added on top of the bracket. ">
-            <param name="start" type="integer" min="0" value="" label="Start" help=""/>
-            <param name="end" type="integer" min="0" value="" label="End" help=""/>
-            <param argument="label" type="text" value="" label="Label" help="">
-                <expand macro="sanitize_query" />
-            </param>
-        </repeat>
-    </xml>
-    <xml name="param_var_group_rotation">
-        <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>
-    </xml>
-    <xml name="param_layer">
-        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default 'adata.raw.X' is plotted. If 'use_raw=False' is set, then 'adata.X' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over 'use_raw'.">
-            <expand macro="sanitize_query" />
-        </param>
-    </xml>
-    <token name="@CMD_param_plot_inputs@"><![CDATA[
-    adata,
-    save='.$format',
-    show=False,
-    ]]></token>
-    <xml name="params_inputs">
-        <expand macro="pl_var_names"/>
-        <expand macro="param_groupby"/>
-        <expand macro="param_num_categories"/>
-    </xml>
-    <token name="@CMD_var_names_header_check@"><![CDATA[
-header='infer'
-#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
-header=None
-#end if
-    ]]></token>
-    <token name="@CMD_params_inputs@"><![CDATA[
-    #if $method.var_names.type == 'custom'
-    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
-    var_names=$var_names,
-    #else if $method.var_names.type == 'customfile'
-    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
-    #else
-    var_names=adata.var_names,
-    #end if
-    #if $method.groupby
-    groupby='$method.groupby',
-    #end if
-    num_categories=$method.num_categories,
-    ]]></token>
-    <xml name="params_plots">
-        <expand macro="param_log"/>
-        <expand macro="param_use_raw"/>
-        <expand macro="param_dendrogram"/>
-        <expand macro="pl_var_group_positions"/>
-        <expand macro="param_var_group_rotation"/>
-        <expand macro="pl_figsize"/>
-        <expand macro="param_layer"/>
-    </xml>
-    <token name="@CMD_params_plots@"><![CDATA[
-    log=$method.log,
-    use_raw=$method.use_raw,
-    dendrogram=$method.dendrogram,
-    #if len($method.var_group_positions) > 0:
-        #set $var_group_positions=[]
-        #set $var_group_labels=[]
-        #for $i, $s in enumerate($method.var_group_positions)
-            #silent $var_group_positions.append((int($s.start), int($s.end)))
-            #silent $var_group_labels.append(str($s.label))
-        #end for
-    var_group_positions=$var_group_positions,
-    var_group_labels=$var_group_labels,
-    #end if
-    #if str($method.var_group_rotation) != ''
-        var_group_rotation=$method.var_group_rotation,
-    #end if
-    #if $method.figsize.test == 'yes'
-        figsize=($method.figsize.width, $method.figsize.height),
-    #end if
-    #if $method.layer
-        layer='$method.layer',
-    #end if
-    ]]></token>
     <xml name="matplotlib_color">
         <option value="AliceBlue">AliceBlue</option>
         <option value="AntiqueWhite">AntiqueWhite</option>
@@ -679,500 +524,298 @@
         <option value="YellowGreen">YellowGreen</option>
     </xml>
     <xml name="param_matplotlib_pyplot_edgecolors">
-        <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
+        <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker">
             <option value="face">The edge color will always be the same as the face color</option>
             <expand macro="matplotlib_color"/>
         </param>
     </xml>
-    <xml name="param_alpha">
-        <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/>
-    </xml>
-    <xml name="param_vmin">
-        <param argument="vmin" type="float" value="" optional="true" label="Minimum value to normalize luminance data" help="If not set, it is inferred from the data and other keyword arguments"/>
-    </xml>
-    <xml name="param_vmax">
-        <param argument="vmax" type="float" value="" optional="true" label="Maximum value to normalize luminance data" help="If not set, it is inferred from the data and other keyword arguments"/>
-    </xml>
-    <xml name="section_matplotlib_pyplot_scatter">
-        <section name="matplotlib_pyplot_scatter" title="Parameters for matplotlib.pyplot.scatter">
-            <!--<param argument="marker" type="select" label="Marker style" help="">
-                <option value="o">o</option>
-                <option value="v">v</option>
-                <option value="^">^</option>
-                <option value="8">8</option>
-                <option value="s">s</option>
-                <option value="p">p</option>
-                <option value="*">*</option>
-                <option value="h">h</option>
-                <option value="H">H</option>
-                <option value="D">D</option>
-                <option value="d">d</option>
-                <option value="P">P</option>
-                <option value="X">X</option>
-            </param>-->
-            <expand macro="param_alpha"/>
-            <expand macro="param_vmin"/>
-            <expand macro="param_vmax"/>
-            <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/>
-            <expand macro="param_matplotlib_pyplot_edgecolors"/>
-        </section>
+    <xml name="param_swap_axes">
+        <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains 'var_names' (e.g. genes) and the y axis the 'groupby' categories (if any). By setting 'swap_axes' then x are the 'groupby' categories and y the 'var_names'."/>
     </xml>
-    <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
-    #if str($method.matplotlib_pyplot_scatter.vmin) != ''
-    vmin=$method.matplotlib_pyplot_scatter.vmin,
-    #end if
-    #if str($method.matplotlib_pyplot_scatter.vmax) != ''
-    vmax=$method.matplotlib_pyplot_scatter.vmax,
-    #end if
-    #if str($method.matplotlib_pyplot_scatter.alpha) != ''
-    alpha=$method.matplotlib_pyplot_scatter.alpha,
-    #end if
-    lw=$method.matplotlib_pyplot_scatter.linewidths,
-    #if $method.matplotlib_pyplot_scatter.edgecolors
-    ec='$method.matplotlib_pyplot_scatter.edgecolors'
-    #end if
-    ]]></token>
-    <xml name="conditional_stripplot">
-        <conditional name="stripplot">
-            <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
-                <option value="True">Yes</option>
-                <option value="False">No</option>
-            </param>
-            <when value="True">
-                <conditional name="jitter">
-                    <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
-                        <option value="True">Yes</option>
-                        <option value="False">No</option>
-                    </param>
-                    <when value="True">
-                        <param argument="size" type="float" min="0" value="1" label="Size of the jitter points" help=""/>
-                    </when>
-                    <when value="False"/>
-                </conditional>
-            </when>
-            <when value="False"/>
-        </conditional>
-    </xml>
-    <token name="@CMD_conditional_stripplot@"><![CDATA[
-    stripplot=$method.violin_plot.stripplot.stripplot,
-#if $method.violin_plot.stripplot.stripplot == "True"
-    jitter=$method.violin_plot.stripplot.jitter.jitter,
-    #if $method.violin_plot.stripplot.jitter.jitter == "True"
-    size=$method.violin_plot.stripplot.jitter.size,
-    #end if
-#end if
-    ]]></token>
-    <xml name="param_scale">
-        <param argument="scale" type="select" label="Method used to scale the width of each violin">
-            <option value="area">area: each violin will have the same area</option>
-            <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
-            <option value="width" selected="true">width: each violin will have the same width</option>
+    <xml name="param_cmap">
+        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups">
+            <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
-    <token name="@CMD_params_violin_plots@"><![CDATA[
-    @CMD_conditional_stripplot@
+    <xml name="param_sort_order">
+        <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
+    </xml>
+    <xml name="param_arrows">
+        <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
+    </xml>
+    <!-- param macros -->
+
+
+    
+    <!-- command macros -->
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
+    </xml>
+    <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[
+| sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
+    ]]>
+    </token>
+    <token name="@CMD_READ_INPUTS@"><![CDATA[
+adata = sc.read_h5ad('anndata.h5ad')
+    ]]>
+    </token>
+    <!-- ln -s doesn't work here because the output is overwritten to the same file -->
+    <token name="@CMD@"><![CDATA[
+cp '$adata' 'anndata.h5ad' &&
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
+    ]]>
+    </token>
+    <token name="@CMD_IMPORTS@"><![CDATA[
+import scanpy as sc
+import pandas as pd
+import numpy as np
+    ]]>
+    </token>
+    <token name="@CMD_ANNDATA_WRITE_OUTPUTS@"><![CDATA[
+adata.write_h5ad('anndata.h5ad', compression='gzip')
+with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
+    print(adata, file=ainfo)
+    ]]>
+    </token>
+    <token name="@CMD_PARAM_PLOT_INPUTS@"><![CDATA[
+    adata,
+    save='.$format',
+    ]]>
+    </token>
+    <token name="@CMD_SHOW_NONE@"><![CDATA[
+        show=None
+        ]]>
+    </token>
+    <token name="@CMD_VAR_NAMES_HEADER_CHECK@"><![CDATA[
+header='infer'
+#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
+header=None
+#end if
+    ]]>
+    </token>
+    <token name="@CMD_PARAMS_VIOLIN_PLOTS@"><![CDATA[
+    @CMD_CONDITIONAL_STRIPPLOT@
     multi_panel=$method.violin_plot.multi_panel.multi_panel,
 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
     figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
 #end if
-    scale='$method.violin_plot.scale',
-    ]]></token>
-    <xml name="seaborn_violinplot">
-        <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
-            <param argument="bw" type="select" label="Name of a reference rule when computing the kernel bandwidth">
-                <option value="scott">scott</option>
-                <option value="silverman">silverman</option>
-            </param>
-            <param argument="orient" type="select" optional="true" label="Orientation of the plot">
-                <option value="v">vertical</option>
-                <option value="h">horizontal</option>
-            </param>
-            <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
-            <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
-                <expand macro="matplotlib_color"/>
-            </param>
-            <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
-        </section>
-    </xml>
-    <token name="@CMD_params_seaborn_violinplot@"><![CDATA[
-    bw='$method.seaborn_violinplot.bw',
-#if $method.seaborn_violinplot.orient
-    orient='$method.seaborn_violinplot.orient',
-#end if
-    linewidth=$method.seaborn_violinplot.linewidth,
-    #if $method.seaborn_violinplot.color
-    color='$method.seaborn_violinplot.color',
-    #end if
-    saturation=$method.seaborn_violinplot.saturation
-    ]]></token>
-    <xml name="param_color">
-        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
-            <expand macro="sanitize_query" />
-        </param>
-    </xml>
-    <token name="@CMD_param_color@"><![CDATA[
-#if $method.color
-    #set $color = ([x.strip() for x in str($method.color).split(',')])
-    color=$color,
-#end if
-    ]]></token>
-    <xml name="param_groups">
-        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
-            <expand macro="sanitize_query" />
+    density_norm='$method.violin_plot.density_norm',
+    ]]>
+    </token>
+    <!-- command macros -->
+
+
+
+    <!-- param and cmd macros -->
+    <xml name="param_standard_scale">
+        <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
+            <option value="None" selected="true">No standardization</option>
+            <option value="var">Standardization on variable</option>
+            <option value="obs">Standardization on observation</option>
         </param>
     </xml>
-    <token name="@CMD_params_groups@"><![CDATA[
-#if $method.groups
-    #set $groups=([x.strip() for x in str($method.groups).split(',')])
-    groups=$groups,
-#end if
-    ]]></token>
-    <xml name="pl_components">
-        <repeat name="components" title="Component">
-            <param argument="axis1" type="text" value="1" label="X-Axis" help="">
-                <expand macro="sanitize_query" />
-            </param>
-            <param argument="axis2" type="text" value="2" label="Y-Axis" help="">
-                <expand macro="sanitize_query" />
-            </param>
-        </repeat>
-    </xml>
-    <token name="@CMD_params_pl_components@"><![CDATA[
-#if len($method.plot.components) > 0
-    #set $components=[]
-    #for $i, $s in enumerate($method.plot.components)
-        #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
-    #end for
-    components=$components,
-#end if
-    ]]>
-    </token>
-    <xml name="param_projection">
-        <param argument="projection" type="select" label="Projection of plot" help="">
-            <option value="2d">2d</option>
-            <option value="3d">3d</option>
-        </param>
-    </xml>
-    <xml name="param_legend_loc">
-        <param argument="legend_loc" type="select" label="Location of legend" help="">
-            <option value="none">none</option>
-            <option value="right margin" selected="true">right margin</option>
-            <option value="on data">on data</option>
-            <option value="on data export">on data export</option>
-            <option value="best">best</option>
-            <option value="upper right">upper right</option>
-            <option value="upper left">upper left</option>
-            <option value="lower left">lower left</option>
-            <option value="lower right">lower right</option>
-            <option value="center left">center left</option>
-            <option value="center right">center right</option>
-            <option value="lower center">lower center</option>
-            <option value="upper center">upper center</option>
-            <option value="center">center</option>
-        </param>
-    </xml>
-    <xml name="param_legend_fontsize">
-        <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/>
-    </xml>
-    <token name="@CMD_param_legend_fontsize@"><![CDATA[
-    #if str($method.plot.legend_fontsize) != ''
-    legend_fontsize=$method.plot.legend_fontsize,
+    <token name="@CMD_STANDARD_SCALE@"><![CDATA[
+    #if str($method.standard_scale) != 'None':
+    standard_scale='$method.standard_scale',
     #end if
     ]]>
     </token>
-    <xml name="param_legend_fontweight">
-        <param argument="legend_fontweight" type="select" label="Legend font weight" help="">
-            <option value="light">light</option>
-            <option value="normal" selected="true">normal</option>
-            <option value="medium">medium</option>
-            <option value="semibold">semibold</option>
-            <option value="bold">bold</option>
-            <option value="heavy">heavy</option>
-            <option value="black">black</option>
-        </param>
-    </xml>
-    <xml name="param_palette">
-        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
-            <expand macro="matplotlib_pyplot_colormap"/>
+
+    <xml name="param_layer" token_optional="true" token_label="If provided, use adata.layers[layer] for expression values instead of adata.X." token_help="">
+        <param argument="layer" type="text" value="" optional="@OPTIONAL@" label="@LABEL@">
+            <expand macro="sanitize_query"/>
         </param>
     </xml>
-    <xml name="param_color_map">
-        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
-            <expand macro="matplotlib_pyplot_colormap"/>
-        </param>
-    </xml>
-    <xml name="param_frameon">
-        <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
-    </xml>
-    <xml name="param_right_margin">
-        <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel" help=""/>
-    </xml>
-    <xml name="param_left_margin">
-        <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/>
-    </xml>
-    <xml name="param_size">
-        <param argument="size" type="float" optional="true" value="" label="Point size" help=""/>
-    </xml>
-    <token name="@CMD_param_size@"><![CDATA[
-    #if str($method.plot.size) != ''
-    size=$method.plot.size,
+    <token name="@CMD_PARAM_LAYER@"><![CDATA[
+    #if str($method.layer) != '':
+    layer='$method.layer',
     #end if
     ]]>
     </token>
-    <xml name="param_title">
-        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma">
-            <expand macro="sanitize_query" />
+
+    <xml name="param_neighbors_key">
+        <param argument="neighbors_key" type="text" value="" label="Key to look for neighbors settings and connectivities" help="If not specified, looks .uns[‘neighbors’] for neighbors settings and .obsp[‘connectivities’] for connectivities (default storage places for pp.neighbors).">
+            <expand macro="sanitize_query"/>
         </param>
     </xml>
-    <token name="@CMD_param_title@"><![CDATA[
-    #if $method.plot.title
-    title='$method.plot.title',
+    <token name="@CMD_PARAM_NEIGHBORS_KEY@"><![CDATA[
+    #if $method.neighbors_key != ''
+    neighbors_key='$method.neighbors_key',
     #end if
     ]]>
     </token>
-    <xml name="param_sort_order">
-        <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
-    </xml>
-    <xml name="param_sort_order">
-        <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
-    </xml>
-    <xml name="param_ncols">
-        <param argument="ncols" type="integer" min="0" value="4" label="Number of panels per row" help=""/>
-    </xml>
-    <xml name="param_wspace">
-        <param argument="wspace" type="float" min="0" value="0.1" label="Width of the space between multiple panels" help=""/>
-    </xml>
-    <xml name="param_hspace">
-        <param argument="hspace" type="float" min="0" value="0.25" label="Height of the space between multiple panels" help=""/>
-    </xml>
-    <xml name="pl_edges">
-        <conditional name="edges">
-            <param argument="edges" type="select" label="Show edges?">
-                <option value="True">Yes</option>
-                <option value="False" selected="true">No</option>
+
+    <xml name="pl_var_names">
+        <conditional name="var_names">
+            <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
+                <option value="all" selected="true">All variables in 'adata.var_names'</option>
+                <option value="custom">Subset of variables in 'adata.var_names'</option>
+                <option value="customfile">Subset of variables as a tabular file</option>
             </param>
-            <when value="True">
-                <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
-                <param argument="edges_color" type="select" optional="true" label="Color of edges">
-                    <expand macro="matplotlib_color"/>
+            <when value="all"/>
+            <when value="custom">
+                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma">
+                    <expand macro="sanitize_query"/>
                 </param>
             </when>
-            <when value="False"/>
+            <when value="customfile">
+                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
+                <param name="header" type="boolean" truevalue="included" falsevalue="not_included" checked="true" label="Header is included in the list of markers?"/>
+            </when>
         </conditional>
     </xml>
-    <token name="@CMD_pl_edges@"><![CDATA[
-#if str($method.edges.edges) == 'True'
-    edges=True,
-    edges_width=$method.edges.edges_width,
-    #if $method.edges.edges_color
-    edges_color='$method.edges.edges_color',
-    #end if
-#else
-    edges=False,
-#end if
-    ]]>
-    </token>
-    <xml name="param_arrows">
-        <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
-    </xml>
-    <xml name="param_cmap">
-        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
-            <expand macro="matplotlib_pyplot_colormap"/>
-        </param>
-    </xml>
-    <xml name="pl_attribute_section">
-        <section name="plot" title="Plot attributes">
-            <expand macro="pl_components"/>
-            <expand macro="param_projection"/>
-            <expand macro="param_legend_loc"/>
-            <expand macro="param_legend_fontsize"/>
-            <expand macro="param_legend_fontweight"/>
-            <expand macro="param_size"/>
-            <expand macro="param_color_map"/>
-            <expand macro="param_palette"/>
-            <expand macro="param_frameon"/>
-            <expand macro="param_ncols"/>
-            <expand macro="param_wspace"/>
-            <expand macro="param_hspace"/>
-            <expand macro="param_title"/>
-        </section>
-    </xml>
-    <token name="@CMD_pl_attribute_section@"><![CDATA[
-    projection='$method.plot.projection',
-    legend_loc='$method.plot.legend_loc',
-    @CMD_param_legend_fontsize@
-    legend_fontweight='$method.plot.legend_fontweight',
-    @CMD_param_size@
-    #if $method.plot.color_map
-    color_map='$method.plot.color_map',
-    #end if
-    #if $method.plot.palette
-    palette='$method.plot.palette',
-    #end if
-    frameon=$method.plot.frameon,
-    ncols=$method.plot.ncols,
-    wspace=$method.plot.wspace,
-    hspace=$method.plot.hspace,
-    @CMD_param_title@
-    ]]>
-    </token>
-    <xml name="options_layout">
-        <option value="fa">fa: ForceAtlas2</option>
-        <option value="fr">fr: Fruchterman-Reingold</option>
-        <option value="grid_fr">grid_fr: Grid Fruchterman Reingold, faster than "fr"</option>
-        <option value="kk">kk: Kamadi Kawai’, slower than "fr"</option>
-        <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
-        <option value="rt">rt: Reingold Tilford tree layout</option>
-        <option value="eq_tree">eq_tree: Equally spaced tree</option>
-    </xml>
-    <xml name="param_layout">
-        <param argument="layout" type="select" label="Plotting layout" optional="false" help="">
-            <expand macro="options_layout"/>
-        </param>
-    </xml>
-    <xml name="param_root">
-        <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">
-            <expand macro="sanitize_query" />
+    <xml name="param_groupby">
+        <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into 'num_categories'.">
+            <expand macro="sanitize_query"/>
         </param>
     </xml>
-    <xml name="param_random_state">
-        <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/>
+    <xml name="param_num_categories">
+        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>
     </xml>
-    <xml name="inputs_paga">
-        <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
-        <expand macro="param_groups"/>
-        <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'.">
-            <expand macro="sanitize_query" />
-        </param>
-        <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/>
-        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed.">
-            <expand macro="sanitize_query" />
-        </param>
-        <expand macro="param_layout"/>
-        <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/>
-        <expand macro="param_random_state"/>
-        <expand macro="param_root"/>
-        <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'">
-            <expand macro="sanitize_query" />
-        </param>
-        <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga">
-            <expand macro="sanitize_query" />
-        </param>
-        <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn.">
-            <expand macro="sanitize_query" />
-        </param>
-        <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
-        <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
-        <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
-        <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/>
-        <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>
-        <param argument="min_edge_width" type="float" min="0" value="" optional="true" label="Min width of solid edges" help=""/>
-        <param argument="max_edge_width" type="float" min="0" value="" optional="true" label="Max width of solid and dashed edges" help=""/>
-        <param argument="arrowsize" type="integer" min="0" value="30" label="Arrow size" help="For directed graphs, choose the size of the arrow head head's length and width."/>
-        <param argument="normalize_to_color" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize categorical plots to color or the underlying grouping?" help=""/>
-        <expand macro="param_cmap"/>
-        <expand macro="param_title"/>
-        <expand macro="param_frameon"/>
+
+    <xml name="params_inputs">
+        <expand macro="pl_var_names"/>
+        <expand macro="param_groupby"/>
+        <expand macro="param_num_categories"/>
     </xml>
-    <token name="@CMD_params_pl_paga@"><![CDATA[
-    threshold=$method.threshold,
-#if $method.groups
-    #set $groups=([x.strip() for x in str($method.groups).split(',')])
-    groups=$groups,
-#end if
-#if $method.color
-    #set $color=([x.strip() for x in str($method.color).split(',')])
-    color=$color,
-#end if
-#if $method.pos
-    pos=np.fromfile($method.pos, dtype=dt),
-#end if
-#if $method.labels
-    #set $labels=([x.strip() for x in str($method.labels).split(',')])
-    labels=$labels,
-#end if
-    layout='$method.layout',
-#if $method.init_pos
-    init_pos=np.fromfile($method.init_pos, dtype=dt),
-#end if
-    random_state=$method.random_state,
-#if $method.root
-    #set $root=([int(x.strip()) for x in str($method.root).split(',')])
-    root=$root,
-#end if
-#if $method.transitions
-    transitions='$method.transitions',
-#end if
-    solid_edges='$method.solid_edges',
-#if $method.dashed_edges
-    dashed_edges='$method.dashed_edges',
-#end if
-    single_component=$method.single_component,
-    fontsize=$method.fontsize,
-    node_size_scale=$method.node_size_scale,
-    node_size_power=$method.node_size_power,
-    edge_width_scale=$method.edge_width_scale,
-#if str($method.min_edge_width) != ''
-    min_edge_width=$method.min_edge_width,
-#end if
-#if str($method.max_edge_width) != ''
-    max_edge_width=$method.max_edge_width,
-#end if
-    arrowsize=$method.arrowsize,
-    normalize_to_color=$method.normalize_to_color,
-    #if $method.cmap
-    cmap='$method.cmap',
+    <token name="@CMD_PARAMS_INPUTS@"><![CDATA[
+    #if str($method.var_names.type) == 'custom':
+    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
+    var_names=$var_names,
+    #else if str($method.var_names.type) == 'customfile':
+    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()},
+    #else
+    var_names=adata.var_names,
+    #end if
+    #if str($method.groupby) != '':
+    groupby='$method.groupby',
     #end if
-#if $method.title
-    title='$method.title',
-#end if
-    frameon=$method.frameon,
+    num_categories=$method.num_categories,
+    ]]>
+    </token>
+
+    <xml name="pl_figsize">
+        <conditional name="figsize">
+            <param name="custom" type="select" label="Custom figure size" >
+                <option value="no" selected="true">No: the figure width is set based on the number of variable names and the height is set to 10.</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param argument="width" type="integer" min="0" value="10" label="Figure width"/>
+                <param argument="height" type="integer" min="0" value="10" label="Figure height"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </xml>
+    <token name="@CMD_PARAMS_FIGSIZE@"><![CDATA[
+    #if $method.figsize.custom == 'yes':
+        figsize=($method.figsize.width, $method.figsize.height),
+    #end if
     ]]>
     </token>
-    <xml name="param_swap_axes">
-        <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains 'var_names' (e.g. genes) and the y axis the 'groupby' categories (if any). By setting 'swap_axes' then x are the 'groupby' categories and y the 'var_names'."/>
+
+    <xml name="param_log" token_checked="false">
+        <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="@CHECKED@" label="Use the log of the values?"/>
+    </xml>
+    <xml name="param_use_raw" token_falsevalue="False">
+        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="@FALSEVALUE@" checked="false" label="Use 'raw' attribute of input if present"/>
+    </xml>
+    <xml name="param_dendrogram">
+        <param argument="dendrogram" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Compute and plot a dendrogram?" help="groupby categories are reordered accoring to the dendrogram order. If groups of var_names are set and those groups correspond to the groupby categories, those groups are also reordered. The ‘person’ method is used to compute the pairwise correlation between categories using all var_names in raw if use_raw is None, otherwise all adata.var_names are used. The linkage method used is complete."/>
     </xml>
-    <xml name="gene_symbols">
-        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
-            <expand macro="sanitize_query" />
-        </param>
+    <xml name="pl_var_group_positions">
+        <repeat name="var_group_positions" title="Group of variables to highlight" help="This will draw a 'bracket' on top of the plot between the given start and end positions. If a label is given, it will be added on top of the bracket. ">
+            <param name="start" type="integer" min="0" value="" label="Start"/>
+            <param name="end" type="integer" min="0" value="" label="End"/>
+            <param argument="label" type="text" value="" label="Label">
+                <expand macro="sanitize_query"/>
+            </param>
+        </repeat>
     </xml>
-    <xml name="param_n_genes">
-        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
+    <xml name="param_var_group_rotation">
+        <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>
     </xml>
-    <xml name="pl_dotplot">
-        <param argument="color_map" type="select" optional="true" label="Color palette">
-            <expand macro="matplotlib_pyplot_colormap"/>
-        </param>
-        <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
-        <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
-        <expand macro="section_matplotlib_pyplot_scatter"/>
+    <xml name="params_plots">
+        <expand macro="param_log"/>
+        <expand macro="param_use_raw" falsevalue="None"/>
+        <expand macro="param_dendrogram"/>
+        <expand macro="pl_var_group_positions"/>
+        <expand macro="param_var_group_rotation"/>
+        <expand macro="pl_figsize"/>
+        <expand macro="param_layer" optional="true" label="Name of the AnnData object layer that wants to be plotted" help="By default 'adata.raw.X' is plotted. If 'use_raw=False' is set, then 'adata.X' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over 'use_raw'."/>
     </xml>
-    <token name="@CMD_pl_dotplot@"><![CDATA[
-    #if $method.color_map
-    color_map='$method.color_map',
+    <token name="@CMD_PARAMS_PLOTS@"><![CDATA[
+    log=$method.log,
+    use_raw=$method.use_raw,
+    dendrogram=$method.dendrogram,
+    #if len($method.var_group_positions) > 0:
+        #set $var_group_positions=[]
+        #set $var_group_labels=[]
+        #for $i, $s in enumerate($method.var_group_positions)
+            #silent $var_group_positions.append((int($s.start), int($s.end)))
+            #silent $var_group_labels.append(str($s.label))
+        #end for
+    var_group_positions=$var_group_positions,
+    var_group_labels=$var_group_labels,
     #end if
-    #if str($method.dot_max) != ''
-    dot_max=$method.dot_max,
+    #if str($method.var_group_rotation) != '':
+        var_group_rotation=$method.var_group_rotation,
     #end if
-    #if str($method.dot_min) != ''
-    dot_min=$method.dot_min,
-    #end if
-    @CMD_params_matplotlib_pyplot_scatter@
+    @CMD_PARAMS_FIGSIZE@
+    @CMD_PARAM_LAYER@
     ]]>
     </token>
-    <xml name="param_key">
-        <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'">
-            <expand macro="sanitize_query" />
-        </param>
+
+    <xml name="param_alpha">
+        <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/>
+    </xml>
+    <xml name="param_vmin" token_label="Minimum value to normalize luminance data" token_help="If not set, it is inferred from the data and other keyword arguments">
+        <param argument="vmin" type="float" value="" optional="true" label="@LABEL@" help="@HELP@"/>
+    </xml>
+    <xml name="param_vmax" token_label="Maximum value to normalize luminance data" token_help="If not set, it is inferred from the data and other keyword arguments">
+        <param argument="vmax" type="float" value="" optional="true" label="@LABEL@" help="@HELP@"/>
+    </xml>
+    <xml name="param_vcenter">
+        <param argument="vcenter" type="float" value="" optional="true" label="The value representing the center of the color scale" help="Useful for diverging colormaps."/>
     </xml>
-    <xml name="pl_heatmap">
+    <xml name="section_matplotlib_pyplot_scatter">
+        <section name="matplotlib_pyplot_scatter" title="Parameters for matplotlib.pyplot.scatter">
+            <expand macro="param_alpha"/>
+            <expand macro="param_vmin"/>
+            <expand macro="param_vmax"/>
+            <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges"/>
+            <expand macro="param_matplotlib_pyplot_edgecolors"/>
+        </section>
+    </xml>
+    <token name="@CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@"><![CDATA[
+    #if str($method.matplotlib_pyplot_scatter.vmin) != '':
+    vmin=$method.matplotlib_pyplot_scatter.vmin,
+    #end if
+    #if str($method.matplotlib_pyplot_scatter.vmax) != '':
+    vmax=$method.matplotlib_pyplot_scatter.vmax,
+    #end if
+    #if str($method.matplotlib_pyplot_scatter.alpha) != '':
+    alpha=$method.matplotlib_pyplot_scatter.alpha,
+    #end if
+    linewidth=$method.matplotlib_pyplot_scatter.linewidths,
+    #if $method.matplotlib_pyplot_scatter.edgecolors:
+    edgecolor='$method.matplotlib_pyplot_scatter.edgecolors',
+    #end if
+    ]]>
+    </token>
+
+    <xml name="params_pl_heatmap">
         <expand macro="param_swap_axes"/>
         <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/>
+        <expand macro="param_standard_scale"/>
         <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
             <expand macro="param_cmap"/>
-            <param name="interpolation" type="select" label="Interpolation method" help="">
-                <option value="None">none</option>
+            <param name="interpolation" type="select" label="Interpolation method">
+                <option value="None" selected="true">none</option>
                 <option value="nearest">nearest</option>
                 <option value="bilinear">bilinear</option>
                 <option value="bicubic">bicubic</option>
@@ -1194,106 +837,627 @@
             <expand macro="param_vmin"/>
             <expand macro="param_vmax"/>
             <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">
-                <option value="upper">Upper</option>
+                <option value="upper" selected="true">Upper</option>
                 <option value="lower">Lower</option>
             </param>
         </section>
     </xml>
-    <token name="@CMD_pl_heatmap@"><![CDATA[
+    <token name="@CMD_PARAMS_PL_HEATMAP@"><![CDATA[
     swap_axes=$method.swap_axes,
     show_gene_labels=$method.show_gene_labels,
-    #if $method.matplotlib_pyplot_imshow.cmap
+    @CMD_STANDARD_SCALE@
+    #if $method.matplotlib_pyplot_imshow.cmap:
     cmap='$method.matplotlib_pyplot_imshow.cmap',
     #end if
-    #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
+    #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None':
     interpolation='$method.matplotlib_pyplot_imshow.interpolation',
     #end if
-    #if str($method.matplotlib_pyplot_imshow.alpha) != ''
+    #if str($method.matplotlib_pyplot_imshow.alpha) != '':
     alpha=$method.matplotlib_pyplot_imshow.alpha,
     #end if
-    #if str($method.matplotlib_pyplot_imshow.vmin) != ''
+    #if str($method.matplotlib_pyplot_imshow.vmin) != '':
     vmin=$method.matplotlib_pyplot_imshow.vmin,
     #end if
-    #if str($method.matplotlib_pyplot_imshow.vmax) != ''
+    #if str($method.matplotlib_pyplot_imshow.vmax) != '':
     vmax=$method.matplotlib_pyplot_imshow.vmax,
     #end if
-    origin='$method.matplotlib_pyplot_imshow.origin'
+    origin='$method.matplotlib_pyplot_imshow.origin',
     ]]>
     </token>
-    <xml name="pl_rank_genes_groups_ext">
-        <expand macro="param_groups"/>
-        <expand macro="param_n_genes"/>
-        <expand macro="param_key"/>
-    </xml>
-    <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
-    @CMD_params_groups@
-    n_genes=$method.n_genes,
-    #if $method.key
-    key='$method.key',
-    #end if
-    ]]>
-    </token>
-    <xml name="pl_matrixplot">
+
+    <xml name="params_pl_matrixplot">
         <expand macro="param_swap_axes"/>
         <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
             <param argument="cmap" type="select" optional="true" label="Color palette">
                 <expand macro="seaborn_color_palette_options"/>
             </param>
-            <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
-            <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
             <expand macro="param_matplotlib_pyplot_edgecolors"/>
             <expand macro="param_alpha"/>
-            <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
+            <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?"/>
         </section>
+        <expand macro="param_standard_scale"/>
+        <expand macro="param_vmin" label="The value representing the lower limit of the color scale" help="Values smaller than vmin are plotted with the same color as vmin."/>
+        <expand macro="param_vmax" label="The value representing the upper limit of the color scale" help="Values larger than vmax are plotted with the same color as vmax."/>
+        <expand macro="param_vcenter"/>
     </xml>
-    <token name="@CMD_pl_matrixplot@"><![CDATA[
+    <token name="@CMD_PARAMS_PL_MATRIXPLOT@"><![CDATA[
     swap_axes=$method.swap_axes,
-    #if $method.matplotlib_pyplot_pcolor.cmap
+    #if $method.matplotlib_pyplot_pcolor.cmap:
     cmap='$method.matplotlib_pyplot_pcolor.cmap',
     #end if
-    #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
-    vmin=$method.matplotlib_pyplot_pcolor.vmin,
+    #if $method.matplotlib_pyplot_pcolor.edgecolors:
+    edgecolor='$method.matplotlib_pyplot_pcolor.edgecolors',
     #end if
-    #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
-    vmax=$method.matplotlib_pyplot_pcolor.vmax,
-    #end if
-    #if $method.matplotlib_pyplot_pcolor.edgecolors
-    ec='$method.matplotlib_pyplot_pcolor.edgecolors',
-    #end if
-    #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
+    #if str($method.matplotlib_pyplot_pcolor.alpha) != '':
     alpha=$method.matplotlib_pyplot_pcolor.alpha,
     #end if
-    snap=$method.matplotlib_pyplot_pcolor.snap
+    snap=$method.matplotlib_pyplot_pcolor.snap,
+    #if str($method.vmin) != '':
+    vmin=$method.vmin,
+    #end if
+    #if str($method.vmax) != '':
+    vmax=$method.vmax,
+    #end if
+    #if str($method.vcenter) != '':
+    vcenter=$method.vcenter,
+    #end if
+    @CMD_STANDARD_SCALE@
+    ]]>
+    </token>
+
+    <xml name="conditional_stripplot">
+        <conditional name="stripplot">
+            <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot">
+                <option value="True" selected="true">Yes</option>
+                <option value="False">No</option>
+            </param>
+            <when value="True">
+                <conditional name="jitter">
+                    <param argument="jitter" type="select" label="Add a jitter to the stripplot">
+                        <option value="True" selected="true">Yes</option>
+                        <option value="False">No</option>
+                    </param>
+                    <when value="True">
+                        <param argument="size" type="float" min="0" value="1" label="Size of the jitter points"/>
+                    </when>
+                    <when value="False"/>
+                </conditional>
+            </when>
+            <when value="False"/>
+        </conditional>
+    </xml>
+    <token name="@CMD_CONDITIONAL_STRIPPLOT@"><![CDATA[
+    stripplot=$method.violin_plot.stripplot.stripplot,
+#if str($method.violin_plot.stripplot.stripplot) == 'True':
+    jitter=$method.violin_plot.stripplot.jitter.jitter,
+    #if str($method.violin_plot.stripplot.jitter.jitter) == 'True':
+    size=$method.violin_plot.stripplot.jitter.size,
+    #end if
+#end if
+    ]]>
+    </token>
+    
+    <xml name="params_seaborn_violinplot">
+        <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
+            <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth">
+                <option value="scott" selected="true">scott</option>
+                <option value="silverman">silverman</option>
+            </param>
+            <param argument="bw_adjust" type="float" value="1" label="Factor that scales the bandwidth to use more or less smoothing."/>
+            <param argument="orient" type="select" optional="true" label="Orientation of the plot">
+                <option value="v">vertical</option>
+                <option value="h">horizontal</option>
+            </param>
+            <param argument="linewidth" type="float" value="" optional="true" label="Width of the gray lines that frame the plot elements"/>
+            <param argument="color" type="select" optional="true" label="Color for all of the elements">
+                <expand macro="matplotlib_color"/>
+            </param>
+            <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at"/>
+        </section>
+    </xml>
+    <token name="@CMD_PARAMS_SEABORN_VIOLINPLOT@"><![CDATA[
+    bw_method='$method.seaborn_violinplot.bw_method',
+    bw_adjust=$method.seaborn_violinplot.bw_adjust,
+    #if $method.seaborn_violinplot.orient:
+    orient='$method.seaborn_violinplot.orient',
+    #end if
+    #if str($method.seaborn_violinplot.linewidth) != '':
+    linewidth=$method.seaborn_violinplot.linewidth,
+    #end if
+    #if $method.seaborn_violinplot.color:
+    color='$method.seaborn_violinplot.color',
+    #end if
+    saturation=$method.seaborn_violinplot.saturation,
+    ]]></token>
+   
+    <xml name="param_color">
+        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
+            <expand macro="sanitize_query"/>
+        </param>
+    </xml>
+    <token name="@CMD_PARAM_COLOR@"><![CDATA[
+#if str($method.color) != '':
+    #set $color = ([x.strip() for x in str($method.color).split(',')])
+    color=$color,
+#end if
+    ]]>
+    </token>
+
+    <xml name="param_groups">
+        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
+            <expand macro="sanitize_query"/>
+        </param>
+    </xml>
+    <token name="@CMD_PARAM_GROUPS@"><![CDATA[
+#if str($method.groups) != '':
+    #set $groups=([x.strip() for x in str($method.groups).split(',')])
+    groups=$groups,
+#end if
+    ]]>
+    </token>
+
+
+    <xml name="param_pl_components">
+        <repeat name="components" title="Component">
+            <param argument="axis1" type="text" value="1" label="X-Axis">
+                <expand macro="sanitize_query"/>
+            </param>
+            <param argument="axis2" type="text" value="2" label="Y-Axis">
+                <expand macro="sanitize_query"/>
+            </param>
+        </repeat>
+    </xml>
+    <token name="@CMD_PARAM_PL_COMPONENTS@"><![CDATA[
+#if len($method.plot.components) > 0:
+    #set $components=[]
+    #for $i, $s in enumerate($method.plot.components)
+        #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
+    #end for
+    components=$components,
+#end if
+    ]]>
+    </token>
+    
+    <xml name="param_legend_fontsize">
+        <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/>
+    </xml>
+    <token name="@CMD_PARAM_LEGEND_FONTSIZE@"><![CDATA[
+    #if str($method.plot.legend_fontsize) != '':
+    legend_fontsize=$method.plot.legend_fontsize,
+    #end if
+    ]]>
+    </token>
+
+    <xml name="param_size">
+        <param argument="size" type="float" optional="true" value="" label="Point size"/>
+    </xml>
+    <token name="@CMD_PARAM_SIZE@"><![CDATA[
+    #if str($method.plot.size) != '':
+    size=$method.plot.size,
+    #end if
+    ]]>
+    </token>
+
+    <xml name="param_title">
+        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma">
+            <expand macro="sanitize_query"/>
+        </param>
+    </xml>
+    <token name="@CMD_PARAM_TITLE@"><![CDATA[
+    #if str($method.plot.title) != '':
+    title='$method.plot.title',
+    #end if
     ]]>
     </token>
-    <xml name="pl_stacked_violin">
+
+    <xml name="param_projection">
+        <param argument="projection" type="select" label="Projection of plot">
+            <option value="2d" selected="true">2d</option>
+            <option value="3d">3d</option>
+        </param>
+    </xml>
+    <xml name="param_legend_loc">
+        <param argument="legend_loc" type="select" label="Location of legend">
+            <yield />
+            <option value="none">none</option>
+            <option value="on data export">on data export</option>
+            <option value="best">best</option>
+            <option value="upper right">upper right</option>
+            <option value="upper left">upper left</option>
+            <option value="lower left">lower left</option>
+            <option value="lower right">lower right</option>
+            <option value="right">right</option>
+            <option value="center left">center left</option>
+            <option value="center right">center right</option>
+            <option value="lower center">lower center</option>
+            <option value="upper center">upper center</option>
+            <option value="center">center</option>
+        </param>
+    </xml>
+    <xml name="param_legend_fontweight">
+        <param argument="legend_fontweight" type="select" label="Legend font weight">
+            <option value="bold" selected="true">bold</option>
+            <option value="normal">normal</option>
+            <option value="light">light</option>
+            <option value="medium">medium</option>
+            <option value="semibold">semibold</option>
+            <option value="heavy">heavy</option>
+            <option value="black">black</option>
+        </param>
+    </xml>
+    <xml name="param_color_map">
+        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables">
+            <expand macro="matplotlib_pyplot_colormap"/>
+        </param>
+    </xml>
+    <xml name="param_palette">
+        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups">
+            <expand macro="matplotlib_pyplot_colormap"/>
+        </param>
+    </xml>
+    <xml name="param_frameon">
+        <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?"/>
+    </xml>
+    <xml name="param_ncols">
+        <param argument="ncols" type="integer" min="0" value="4" label="Number of panels per row"/>
+    </xml>
+    <xml name="param_wspace">
+        <param argument="wspace" type="float" min="0" value="0.1" label="Width of the space between multiple panels"/>
+    </xml>
+    <xml name="param_hspace">
+        <param argument="hspace" type="float" min="0" value="0.25" label="Height of the space between multiple panels"/>
+    </xml>
+
+    <xml name="params_pl_attribute_section">
+        <section name="plot" title="Plot attributes">
+            <expand macro="param_pl_components"/>
+            <expand macro="param_projection"/>
+            <expand macro="param_legend_loc">
+                <option value="right margin">right margin</option>
+                <option value="on data">on data</option>
+            </expand>
+            <expand macro="param_legend_fontsize"/>
+            <expand macro="param_legend_fontweight"/>
+            <expand macro="param_size"/>
+            <expand macro="param_color_map"/>
+            <expand macro="param_palette"/>
+            <expand macro="param_frameon"/>
+            <expand macro="param_ncols"/>
+            <expand macro="param_wspace"/>
+            <expand macro="param_hspace"/>
+            <expand macro="param_title"/>
+        </section>
+    </xml>
+    <token name="@CMD_PARAMS_PL_ATTRIBUTE_SECTION@"><![CDATA[
+    @CMD_PARAM_PL_COMPONENTS@
+    projection='$method.plot.projection',
+    #if str($method.plot.legend_loc) != '':
+    legend_loc='$method.plot.legend_loc',
+    #end if
+    @CMD_PARAM_LEGEND_FONTSIZE@
+    legend_fontweight='$method.plot.legend_fontweight',
+    @CMD_PARAM_SIZE@
+    #if $method.plot.color_map:
+    color_map='$method.plot.color_map',
+    #end if
+    #if $method.plot.palette:
+    palette='$method.plot.palette',
+    #end if
+    frameon=$method.plot.frameon,
+    ncols=$method.plot.ncols,
+    wspace=$method.plot.wspace,
+    hspace=$method.plot.hspace,
+    @CMD_PARAM_TITLE@
+    ]]>
+    </token>
+
+    <xml name="pl_edges">
+        <conditional name="edges">
+            <param argument="edges" type="select" label="Show edges?">
+            	<option value="False" selected="true">No</option>
+                <option value="True">Yes</option>
+            </param>
+            <when value="True">
+                <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
+                <param argument="edges_color" type="select" optional="true" label="Color of edges">
+                    <expand macro="matplotlib_color"/>
+                </param>
+            </when>
+            <when value="False"/>
+        </conditional>
+    </xml>
+    <token name="@CMD_PL_EDGES@"><![CDATA[
+#if str($method.edges.edges) == 'True':
+    edges=True,
+    edges_width=$method.edges.edges_width,
+    #if $method.edges.edges_color:
+    edges_color='$method.edges.edges_color',
+    #end if
+#else
+    edges=False,
+#end if
+    ]]>
+    </token>
+
+
+    <xml name="options_layout">
+    	<option value="fa" selected="true">fa: ForceAtlas2</option>
+        <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
+        <option value="fr">fr: Fruchterman-Reingold</option>
+        <option value="grid_fr">grid_fr: Grid Fruchterman Reingold, faster than "fr"</option>
+        <option value="kk">kk: Kamadi Kawai’, slower than "fr"</option>
+        <option value="lgl">Large Graph, very fast</option>
+        <option value="rt">rt: Reingold Tilford tree layout</option>
+        <option value="rt_circular">rt_circular: Reingold Tilford tree circular</option>
+    </xml>
+    <xml name="param_layout">
+        <param argument="layout" type="select" label="Plotting layout" optional="false">
+            <expand macro="options_layout"/>
+        </param>
+    </xml>
+    <xml name="params_pl_paga">
+        <param argument="threshold" type="float" min="0" value="" optional="true" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
+        <expand macro="param_groups"/>
+        <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'.">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing"/>
+        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed.">
+            <expand macro="sanitize_query"/>
+        </param>
+        <expand macro="param_layout"/>
+        <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout"/>
+        <param argument="random_state" type="integer" value="0" label="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/>
+        <param argument="root" type="text" value="0" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn.">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?"/>
+        <param argument="fontsize" type="integer" min="0" value="" optional="true" label="Font size for node labels"/>
+        <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes"/>
+        <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes"/>
+        <param argument="edge_width_scale" type="float" min="0" value="1.0" label="Scale for edge width"/>
+        <param argument="min_edge_width" type="float" min="0" value="" optional="true" label="Min width of solid edges"/>
+        <param argument="max_edge_width" type="float" min="0" value="" optional="true" label="Max width of solid and dashed edges"/>
+        <param argument="arrowsize" type="integer" min="0" value="30" label="Arrow size" help="For directed graphs, choose the size of the arrow head head's length and width."/>
+        <param argument="normalize_to_color" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize categorical plots to color or the underlying grouping?"/>
+        <expand macro="param_cmap"/>
+        <expand macro="param_title"/>
+        <expand macro="param_frameon"/>
+    </xml>
+    <token name="@CMD_PARAMS_PL_PAGA@"><![CDATA[
+        #if str($method.threshold) != '':
+    threshold=$method.threshold,
+        #end if
+        #if str($method.groups) != '':
+            #set $groups=([x.strip() for x in str($method.groups).split(',')])
+    groups=$groups,
+        #end if
+        #if str($method.color) != '':
+            #set $color=([x.strip() for x in str($method.color).split(',')])
+    color=$color,
+        #end if
+        #if $method.pos:
+    pos=np.fromfile($method.pos, dtype=dt),
+        #end if
+        #if str($method.labels) != '':
+            #set $labels=([x.strip() for x in str($method.labels).split(',')])
+    labels=$labels,
+        #end if
+    layout='$method.layout',
+        #if $method.init_pos:
+    init_pos=np.fromfile($method.init_pos, dtype=dt),
+        #end if
+    random_state=$method.random_state,
+        #if str($method.root) != '':
+            #set $root=([int(x.strip()) for x in str($method.root).split(',')])
+    root=$root,
+        #end if
+        #if str($method.transitions) != '':
+    transitions='$method.transitions',
+        #end if
+    solid_edges='$method.solid_edges',
+        #if str($method.dashed_edges) != '':
+    dashed_edges='$method.dashed_edges',
+        #end if
+    single_component=$method.single_component,
+    fontsize=$method.fontsize,
+    node_size_scale=$method.node_size_scale,
+    node_size_power=$method.node_size_power,
+    edge_width_scale=$method.edge_width_scale,
+        #if str($method.min_edge_width) != '':
+    min_edge_width=$method.min_edge_width,
+        #end if
+        #if str($method.max_edge_width) != '':
+    max_edge_width=$method.max_edge_width,
+        #end if
+    arrowsize=$method.arrowsize,
+    normalize_to_color=$method.normalize_to_color,
+    #if $method.cmap:
+    cmap='$method.cmap',
+    #end if
+        #if str($method.title) != '':
+    title='$method.title',
+        #end if
+    frameon=$method.frameon,
+    ]]>
+    </token>
+
+    <xml name="param_gene_symbols">
+        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols" help="By default 'var_names' refer to the index column of the '.var' DataFrame">
+            <expand macro="sanitize_query"/>
+        </param>
+    </xml>
+    <token name="@CMD_PARAM_GENE_SYMBOLS@"><![CDATA[
+    #if str($method.gene_symbols) != '':
+    gene_symbols='$method.gene_symbols',
+    #end if
+    ]]>
+    </token>
+
+    <xml name="params_pl_dotplot">
+        <param argument="color_map" type="select" optional="true" label="Color palette">
+            <expand macro="matplotlib_pyplot_colormap"/>
+        </param>
+        <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
+        <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
+        <expand macro="param_standard_scale"/>
+        <param argument="expression_cutoff" type="float" min="0.0" value="0.0" label="Expression cutoff that is used for binarizing the gene expression and determining the fraction of cells expressing given genes" help="A gene is expressed only if the expression value is greater than this threshold."/>
+        <param argument="mean_only_expressed" type="boolean" truevalue="True" falsevalue="False" checked="false" label="average the gene expression only over the cells expressing the given genes"/>
+        <expand macro="section_matplotlib_pyplot_scatter"/>
+    </xml>
+    <token name="@CMD_PL_DOTPLOT@"><![CDATA[
+    #if $method.color_map:
+    color_map='$method.color_map',
+    #end if
+    #if str($method.dot_max) != '':
+    dot_max=$method.dot_max,
+    #end if
+    #if str($method.dot_min) != '':
+    dot_min=$method.dot_min,
+    #end if
+    @CMD_STANDARD_SCALE@
+    expression_cutoff=$method.expression_cutoff,
+    mean_only_expressed=$method.mean_only_expressed,
+    @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
+    ]]>
+    </token>
+
+    <xml name="values_to_plot">
+        <param argument="values_to_plot" type="select" optional="true" label="Values to plot" help="Defualt: plots mean expression. When plotting logfoldchanges a divergent colormap is recommended.">
+            <option value="scores">Scores</option>
+            <option value="logfoldchanges">Log foldchanges</option>
+            <option value="pvals">P-values</option>
+            <option value="pvals_adj">Adjusted p-values</option>
+            <option value="log10_pvals">log10 of p-values</option>
+            <option value="log10_pvals_adj">log10 of adjusted p-values</option>
+        </param>
+    </xml>
+    <token name="@CMD_VALUES_TO_PLOT@"><![CDATA[
+    #if $method.values_to_plot:
+    values_to_plot='$method.values_to_plot',
+    colorbar_title='$method.values_to_plot',
+    #end if
+    ]]>
+    </token>
+
+
+    <xml name="param_n_genes" token_value="">
+        <param argument="n_genes" type="integer" min="0" value="@VALUE@" optional="true" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
+    </xml>
+    <xml name="param_key">
+        <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'">
+            <expand macro="sanitize_query"/>
+        </param>
+    </xml>
+
+    <xml name="pl_rank_genes_groups_ext">
+        <expand macro="pl_var_names"/>
+        <expand macro="param_groups"/>
+        <expand macro="param_n_genes" value=""/>
+        <expand macro="param_key"/>
+        <param argument="min_logfoldchange" type="integer" optional="true" value="" label="Value to filter genes in groups if their logfoldchange is less than this value"/>
+    </xml>
+    <token name="@CMD_PL_RANK_GENES_GROUPS_EXT@"><![CDATA[
+    #if str($method.var_names.type) == 'custom':
+    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
+    var_names=$var_names,
+    #else if str($method.var_names.type) == 'customfile':
+    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()},
+    #end if
+    @CMD_PARAM_GROUPS@
+    #if str($method.n_genes) != '':
+    n_genes=$method.n_genes,
+    #end if
+    #if str($method.key) != '':
+    key='$method.key',
+    #end if
+    #if str($method.min_logfoldchange) != '':
+    min_logfoldchange=$method.min_logfoldchange,
+    #end if
+    ]]>
+    </token>
+
+    <xml name="param_density_norm">
+        <param argument="density_norm" type="select" label="Method used to scale the width of each violin">
+        	<option value="area" selected="true">area: each violin will have the same area</option>
+            <option value="width">width: each violin will have the same width</option>
+            <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
+        </param>
+    </xml>
+    <xml name="params_pl_stacked_violin">
         <expand macro="param_swap_axes"/>
         <section name="violin_plot" title="Violin plot attributes">
             <expand macro="conditional_stripplot"/>
-            <expand macro="param_scale"/>
+            <expand macro="param_density_norm"/>
         </section>
         <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
             <option value="muted">muted</option>
             <expand macro="seaborn_color_palette_options"/>
         </param>
-        <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
-            <option value="None">No standardization</option>
-            <option value="var">Standardization on variable</option>
-            <option value="obs">Standardization on observation</option>
-        </param>
-        <expand macro="seaborn_violinplot"/>
+        <expand macro="param_standard_scale"/>
+        <expand macro="params_seaborn_violinplot"/>
+        <param argument="yticklabels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Set to view the y tick labels"/>
+        <expand macro="param_vmin" label="The value representing the lower limit of the color scale" help="Values smaller than vmin are plotted with the same color as vmin."/>
+        <expand macro="param_vmax" label="The value representing the upper limit of the color scale" help="Values larger than vmax are plotted with the same color as vmax."/>
+        <expand macro="param_vcenter"/>
     </xml>
-    <token name="@CMD_pl_stacked_violin@"><![CDATA[
+    <token name="@CMD_PARAMS_PL_STACKED_VIOLIN@"><![CDATA[
     swap_axes=$method.swap_axes,
-    @CMD_conditional_stripplot@
-    scale='$method.violin_plot.scale',
-    #if $method.row_palette
+    @CMD_CONDITIONAL_STRIPPLOT@
+    density_norm='$method.violin_plot.density_norm',
+    #if $method.row_palette:
     row_palette='$method.row_palette',
     #end if
-    #if str($method.standard_scale) != 'None'
-    standard_scale='$method.standard_scale',
+    @CMD_STANDARD_SCALE@
+    @CMD_PARAMS_SEABORN_VIOLINPLOT@
+    yticklabels=$method.yticklabels,
+    #if str($method.vmin) != '':
+    vmin=$method.vmin,
     #end if
-    @CMD_params_seaborn_violinplot@
+    #if str($method.vmax) != '':
+    vmax=$method.vmax,
+    #end if
+    #if str($method.vcenter) != '':
+    vcenter=$method.vcenter,
+    #end if
     ]]>
     </token>
+
+    <xml name="params_scatter_outine">
+        <param argument="add_outline" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Add a thin border around groups of dots" help="In some situations this can enhance the aesthetics of the resulting image"/>
+        <param name="outline_color_border" type="select" optional="true" label="Border color around the scatter dot" help="Default: black">
+            <expand macro="matplotlib_color"/>
+        </param>
+        <param name="outline_color_gap" type="select" optional="true" label="Gap color between the border color and the scatter dot" help="Default: white">
+            <expand macro="matplotlib_color"/>
+        </param>
+        <param argument="outline_width_border" type="float" value="0.3" optional="true" label=" width of the border color as a fraction of the scatter dot size "/>
+        <param argument="outline_width_gap" type="float" value="0.05" optional="true" label="The width of the gap color"/>
+    </xml>
+    <token name="@CMD_SCATTER_OUTINE@"><![CDATA[
+    add_outline=$method.add_outline,
+    #if $method.outline_color_border and $method.outline_color_gap:
+    outline_color=($method.outline_color_border, $method.outline_color_gap),
+    #end if
+    outline_width=($method.outline_width_border, $method.outline_width_gap),
+    ]]>
+    </token>
+
+
+    <!-- unused macros -->
+    <!-- <xml name="param_right_margin">
+        <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel"/>
+    </xml>
+    <xml name="param_left_margin">
+        <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel"/>
+    </xml> -->
 </macros>
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