# HG changeset patch
# User iuc
# Date 1716477598 0
# Node ID 8f8bef61fd0b02e008b9fc98619f4c47c8a0c521
# Parent  af821711b356a23f98f72d1b6536a06b234df301
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snapatac2 commit 1e34deee1e39c0c65e1e29a9d28becc7aaf23a4f

diff -r af821711b356 -r 8f8bef61fd0b dimension_reduction_clustering.xml
--- a/dimension_reduction_clustering.xml	Thu May 16 13:15:57 2024 +0000
+++ b/dimension_reduction_clustering.xml	Thu May 23 15:19:58 2024 +0000
@@ -18,127 +18,130 @@
 @CMD_read_inputs@
 
 #if $method.method == 'tl.spectral'
-	#if $method.features
+    #if $method.features
 with open('$method.features') as f:
-	features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]
-	#end if
+    features_mask = [x.lower().capitalize() == "True" for x in f.read().splitlines()]
+    #end if
 sa.tl.spectral(
-	adata,
-	n_comps = $method.n_comps,
-	#if $method.features
-	features = features_mask,
-	#end if
-	random_state = $method.random_state,
-	#if $method.sample_size
-	sample_size = $method.sample_size,
-	#end if
-	chunk_size = $method.chunk_size,
-	distance_metric = '$method.distance_metric',
-	weighted_by_sd = $method.weighted_by_sd,
-	inplace = True
+    adata,
+    n_comps = $method.n_comps,
+    #if $method.features
+    features = features_mask,
+    #end if
+    random_state = $method.random_state,
+    #if $method.sample_size
+    sample_size = $method.sample_size,
+    #end if
+    chunk_size = $method.chunk_size,
+    distance_metric = '$method.distance_metric',
+    weighted_by_sd = $method.weighted_by_sd,
+    inplace = True
 )
 
 #else if $method.method == 'tl.umap'
 sa.tl.umap(
-	adata,
-	n_comps = $method.n_comps,
-	#if $method.use_dims != ''
-	    #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
-	use_dims=$dims,
-	#end if
-	use_rep = '$method.use_rep',
-	key_added = '$method.key_added',
-	random_state = $method.random_state,
-	inplace = True
+    adata,
+    n_comps = $method.n_comps,
+    #if $method.use_dims != ''
+        #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
+    use_dims=$dims,
+    #end if
+    use_rep = '$method.use_rep',
+    key_added = '$method.key_added',
+    random_state = $method.random_state,
+    inplace = True
 )
 
 #else if $method.method == 'pp.knn'
 sa.pp.knn(
-	adata,
-	n_neighbors = $method.n_neighbors,
-	#if $method.use_dims != ''
-	    #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
-	use_dims=$dims,
-	#end if
-	use_rep = '$method.use_rep',
-	method = '$method.algorithm',
-	inplace = True,
-	random_state = $method.random_state
+    adata,
+    n_neighbors = $method.n_neighbors,
+    #if $method.use_dims != ''
+        #set $dims = ([x.strip() for x in str($method.use_dims).split(',')])
+    use_dims=$dims,
+    #end if
+    use_rep = '$method.use_rep',
+    method = '$method.algorithm',
+    inplace = True,
+    random_state = $method.random_state
 )
 
 #else if $method.method == 'tl.dbscan'
 sa.tl.dbscan(
-	adata,
-	eps = $method.eps,
-	min_samples = $method.min_samples,
-	leaf_size = $method.leaf_size,
-	use_rep = '$method.use_rep',
-	key_added = '$method.key_added'
+    adata,
+    eps = $method.eps,
+    min_samples = $method.min_samples,
+    leaf_size = $method.leaf_size,
+    use_rep = '$method.use_rep',
+    key_added = '$method.key_added'
 )
 
 #else if $method.method == 'tl.hdbscan'
 sa.tl.hdbscan(
-	adata,
-	min_cluster_size = $method.min_cluster_size,
-	#if $method.min_samples
-	min_samples = $method.min_samples,
-	#end if
-	cluster_selection_epsilon = $method.cluster_selection_epsilon,
-	alpha = $method.alpha,
-	cluster_selection_method = '$method.cluster_selection_method',
-	random_state = $method.random_state,
-	use_rep = '$method.use_rep',
-	key_added = '$method.key_added'
+    adata,
+    min_cluster_size = $method.min_cluster_size,
+    #if $method.min_samples
+    min_samples = $method.min_samples,
+    #end if
+    cluster_selection_epsilon = $method.cluster_selection_epsilon,
+    alpha = $method.alpha,
+    cluster_selection_method = '$method.cluster_selection_method',
+    random_state = $method.random_state,
+    use_rep = '$method.use_rep',
+    key_added = '$method.key_added'
 )
 
 #else if $method.method == 'tl.leiden'
 sa.tl.leiden(
-	adata,
-	resolution = $method.resolution,
-	objective_function = '$method.objective_function',
-	min_cluster_size = $method.min_cluster_size,
-	n_iterations = $method.n_iterations,
-	random_state = $method.random_state,
-	key_added = '$method.key_added',
-	weighted = $method.weighted,
-	inplace = True
+    adata,
+    resolution = $method.resolution,
+    objective_function = '$method.objective_function',
+    #if $method.objective_function == 'RBConfiguration'
+    use_leidenalg = True,
+    #end if
+    min_cluster_size = $method.min_cluster_size,
+    n_iterations = $method.n_iterations,
+    random_state = $method.random_state,
+    key_added = '$method.key_added',
+    weighted = $method.weighted,
+    inplace = True
 )
 
 #else if $method.method == 'tl.kmeans'
 sa.tl.kmeans(
-	adata,
-	n_clusters = $method.n_clusters,
-	n_iterations = $method.n_iterations,
-	random_state = $method.random_state,
-	use_rep = '$method.use_rep',
-	key_added = '$method.key_added'
+    adata,
+    n_clusters = $method.n_clusters,
+    n_iterations = $method.n_iterations,
+    random_state = $method.random_state,
+    use_rep = '$method.use_rep',
+    key_added = '$method.key_added'
 )
 
 #else if $method.method == 'tl.aggregate_X'
 sa.tl.aggregate_X(
-	adata,
-	#if $method.groupby != ''
-	groupby = '$method.groupby',
-	#end if
-	normalize = '$method.normalize'
+    adata,
+    #if $method.groupby != ''
+    groupby = '$method.groupby',
+    #end if
+    normalize = '$method.normalize'
 )
 
 #else if $method.method == 'tl.aggregate_cells'
 sa.tl.aggregate_cells(
-	adata,
-	use_rep = '$method.use_rep',
-	#if $method.target_num_cells
-	target_num_cells = $method.target_num_cells,
-	#end if
-	min_cluster_size = $method.min_cluster_size,
-	random_state = $method.random_state,
-	key_added = '$method.key_added',
-	inplace = True
+    adata,
+    use_rep = '$method.use_rep',
+    #if $method.target_num_cells
+    target_num_cells = $method.target_num_cells,
+    #end if
+    min_cluster_size = $method.min_cluster_size,
+    random_state = $method.random_state,
+    key_added = '$method.key_added',
+    inplace = True
 )
 #end if
 
 @CMD_anndata_write_outputs@
-	]]></configfile>
+    ]]></configfile>
     </configfiles>
     <inputs>
         <conditional name="method">
@@ -162,7 +165,7 @@
                 <param argument="chunk_size" type="integer" value="20000" label="chunk size"/>
                 <param argument="distance_metric" type="select" label="distance metric: “jaccard”, “cosine“">
                     <option value="jaccard">jaccard</option>
-                    <option value="cosine">cosine</option>
+                    <option value="cosine" selected="true">cosine</option>
                 </param>
                 <param argument="weighted_by_sd" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Whether to weight the result eigenvectors by the square root of eigenvalues"/>
             </when>
@@ -195,7 +198,7 @@
                 <param argument="resolution" type="float" value="1" label="Parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters"/>
                 <param argument="objective_function" type="select" label="Whether to use the Constant Potts Model (CPM) or modularity">
                     <option value="CPM">CPM</option>
-                    <option value="modularity">modularity</option>
+                    <option value="modularity" selected="true">modularity</option>
                     <option value="RBConfiguration">RBConfiguration</option>
                 </param>
                 <param argument="min_cluster_size" type="integer" value="5" label="The minimum size of clusters"/>
@@ -267,7 +270,7 @@
             <!-- tl.spectral -->
             <conditional name="method">
                 <param name="method" value="tl.spectral"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/pp.select_features.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.select_features.pbmc_500_chr21.h5ad"/>
                 <param name="n_comps" value="30"/>
                 <param name="random_state" value="0"/>
                 <param name="chunk_size" value="20000"/>
@@ -287,13 +290,13 @@
                     <has_text_matching expression="weighted_by_sd = True"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.umap -->
             <conditional name="method">
                 <param name="method" value="tl.umap"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="n_comps" value="2"/>
                 <param name="use_rep" value="X_spectral"/>
                 <param name="key_added" value="umap"/>
@@ -311,13 +314,13 @@
                     <has_text_matching expression="random_state = 0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.umap.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.umap.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- pp.knn -->
             <conditional name="method">
                 <param name="method" value="pp.knn"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.umap.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.umap.pbmc_500_chr21.h5ad"/>
                 <param name="n_neighbors" value="50"/>
                 <param name="use_rep" value="X_spectral"/>
                 <param name="method_" value="kdtree"/>
@@ -337,13 +340,13 @@
                     <has_text_matching expression="random_state = 0"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/pp.knn.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/pp.knn.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.leiden -->
             <conditional name="method">
                 <param name="method" value="tl.leiden"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/pp.knn.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.knn.pbmc_500_chr21.h5ad"/>
                 <param name="resolution" value="2"/>
                 <param name="objective_function" value="modularity"/>
                 <param name="min_cluster_size" value="3"/>
@@ -367,13 +370,43 @@
                     <has_text_matching expression="weighted = False"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.leiden.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.leiden.modularity.pbmc_500_chr21.h5ad"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- tl.leiden -->
+            <conditional name="method">
+                <param name="method" value="tl.leiden"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/pp.knn.pbmc_500_chr21.h5ad"/>
+                <param name="resolution" value="2"/>
+                <param name="objective_function" value="RBConfiguration"/>
+                <param name="min_cluster_size" value="3"/>
+                <param name="n_iterations" value="-1"/>
+                <param name="random_state" value="0"/>
+                <param name="key_added" value="leiden"/>
+                <param name="weighted" value="False"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="sa.tl.leiden"/>
+                    <has_text_matching expression="resolution = 2"/>
+                    <has_text_matching expression="objective_function = 'RBConfiguration'"/>
+                    <has_text_matching expression="min_cluster_size = 3"/>
+                    <has_text_matching expression="n_iterations = -1"/>
+                    <has_text_matching expression="random_state = 0"/>
+                    <has_text_matching expression="key_added = 'leiden'"/>
+                    <has_text_matching expression="weighted = False"/>
+                </assert_contents>
+            </output>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.leiden.RBConfiguration.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.kmeans -->
             <conditional name="method">
                 <param name="method" value="tl.kmeans"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="n_iterations" value="-1"/>
                 <param name="random_state" value="0"/>
                 <param name="use_rep" value="X_spectral"/>
@@ -391,13 +424,13 @@
                     <has_text_matching expression="key_added = 'kmeans'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.kmeans.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.kmeans.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.dbscan -->
             <conditional name="method">
                 <param name="method" value="tl.dbscan"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="eps" value="0.5"/>
                 <param name="min_samples" value="3"/>
                 <param name="leaf_size" value="5"/>
@@ -417,13 +450,13 @@
                     <has_text_matching expression="key_added = 'dbscan'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.dbscan.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.dbscan.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.hdbscan -->
             <conditional name="method">
                 <param name="method" value="tl.hdbscan"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="min_cluster_size" value="3"/>
                 <param name="min_samples" value="3"/>
                 <param name="cluster_selection_method" value="eom"/>
@@ -445,13 +478,13 @@
                     <has_text_matching expression="key_added = 'hdbscan'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.hdbscan.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.hdbscan.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.aggregate_X -->
             <conditional name="method">
                 <param name="method" value="tl.aggregate_X"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="normalize" value="RPKM"/>
             </conditional>
             <section name="advanced_common">
@@ -463,13 +496,13 @@
                     <has_text_matching expression="normalize = 'RPKM'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_X.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.aggregate_X.pbmc_500_chr21.h5ad"/>
         </test>
         <test expect_num_outputs="2">
             <!-- tl.aggregate_cells -->
             <conditional name="method">
                 <param name="method" value="tl.aggregate_cells"/>
-                <param name="adata" location="https://zenodo.org/records/11199963/files/tl.spectral.pbmc_500_chr21.h5ad"/>
+                <param name="adata" location="https://zenodo.org/records/11260316/files/tl.spectral.pbmc_500_chr21.h5ad"/>
                 <param name="use_rep" value="X_spectral"/>
                 <param name="target_num_cells" value="5"/>
                 <param name="min_cluster_size" value="3"/>
@@ -489,7 +522,7 @@
                     <has_text_matching expression="key_added = 'pseudo_cell'"/>
                 </assert_contents>
             </output>
-            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11199963/files/tl.aggregate_cells.pbmc_500_chr21.h5ad"/>
+            <output name="anndata_out" ftype="h5ad" compare="sim_size" delta_frac="0.1" location="https://zenodo.org/records/11260316/files/tl.aggregate_cells.pbmc_500_chr21.h5ad"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r af821711b356 -r 8f8bef61fd0b macros.xml
--- a/macros.xml	Thu May 16 13:15:57 2024 +0000
+++ b/macros.xml	Thu May 23 15:19:58 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-	<token name="@TOOL_VERSION@">2.5.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">2.5.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">snapatac2</requirement>
@@ -12,6 +12,9 @@
         <requirement type="package" version="0.8.33">hdbscan</requirement>
         <requirement type="package" version="0.0.9">harmonypy</requirement>
         <requirement type="package" version="1.7.4">scanorama</requirement>
+        <requirement type="package" version="3.0.1">macs3</requirement>
+        <requirement type="package" version="0.70.16">multiprocess</requirement>
+        <requirement type="package" version="0.10.2">leidenalg</requirement>
         <yield />
     </xml>
 
@@ -23,8 +26,8 @@
     <token name="@CMD@"><![CDATA[
         cat '$script_file' > '$hidden_output' &&
         python '$script_file' >> '$hidden_output' &&
-		touch 'anndata_info.txt' &&
-		cat 'anndata_info.txt' @CMD_prettify_stdout@
+        touch 'anndata_info.txt' &&
+        cat 'anndata_info.txt' @CMD_prettify_stdout@
         ]]>
     </token>
 
@@ -56,7 +59,7 @@
 
     <xml name="dimentions_plot">
         <param argument="width" type="integer" value="500" label="Width of the plot"/>
-		<param argument="height" type="integer" value="400" label="Height of the plot"/>
+        <param argument="height" type="integer" value="400" label="Height of the plot"/>
     </xml>
 
     <xml name="param_groupby">
@@ -66,11 +69,11 @@
     </xml>
 
     <xml name="out_file">
-        <param name="out_file" type="select" optional="true" label="Type of output file">
+        <param name="out_file" type="select" optional="true" label="Type of output plot">
             <option value="png" selected="true">PNG</option>
             <option value="svg">SVG</option>
             <option value="pdf">PDF</option>
-		</param>
+        </param>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
 adata.write('anndata.h5ad')
@@ -89,28 +92,28 @@
         <expand macro="out_file"/>
     </xml>
     <xml name="param_shift">
-    	<param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
-    	<param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
+        <param argument="shift_left" type="integer" value="4" label="Insertion site correction for the left end" help="Note this has no effect on single-end reads"/>
+        <param argument="shift_right" type="integer" value="-5" label="Insertion site correction for the right end" help="Note this has no effect on single-end reads"/>
     </xml>
     <xml name="param_chunk_size" tokens="size">
-    	<param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
+        <param argument="chunk_size" type="integer" value="@SIZE@" label="chunk size"/>
+    </xml>
+    <xml name="min_max_frag_size">
+        <param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
+        <param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
     </xml>
-	<xml name="min_max_frag_size">
-		<param argument="min_frag_size" type="integer" optional="true" value="" label="Minimum fragment size to include"/>
-		<param argument="max_frag_size" type="integer" optional="true" value="" label="Maximum fragment size to include"/>
-	</xml>
-	<xml name="params_data_integration">
-		<param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
-		<param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
-			<expand macro="sanitize_query"/>
-		</param>
-		<param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
+    <xml name="params_data_integration">
+        <param argument="use_rep" type="text" value="X_spectral" label="The key for the matrix"/>
+        <param argument="use_dims" type="text" optional="true" value="" label="The dimensions used for computation">
+            <expand macro="sanitize_query"/>
+        </param>
+        <param argument="groupby" type="text" optional="true" value="" label="The key of the observation grouping to consider">
             <expand macro="sanitize_query" />
         </param>
-		<param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
-	</xml>
+        <param argument="key_added" type="text" optional="true" value="" label="If specified, add the result to adata.obsm with this key"/>
+    </xml>
     <xml name="param_n_comps">
-s        <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
+        <param argument="n_comps" type="integer" value="30" label="Number of dimensions to keep" help="The result is insensitive to this parameter when `weighted_by_sd` is set, as long as it is large enough, e.g. 30."/>
     </xml>
     <xml name="param_random_state">
         <param argument="random_state" type="integer" value="0" label="Seed of the random state generator"/>
@@ -126,12 +129,12 @@
     </xml>
     <xml name="background">
         <param argument="background" type="text" optional="true" value="" label="A list of regions to be used as the background">
-			<expand macro="sanitize_query"/>
-		</param>
+            <expand macro="sanitize_query"/>
+        </param>
     </xml>
     <xml name="mat">
         <param argument="peak_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by peak count matrix"/>
-		<param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
+        <param argument="gene_mat" type="data" format="h5ad" optional="true" label="AnnData or AnnDataSet object storing the cell by gene count matrix"/>
     </xml>
     <xml name="param_network">
         <param argument="network" type="text" label="network"/>
@@ -147,11 +150,11 @@
         </citations>
     </xml>
     <xml name="render_plot_test">
-    	<param name="width" value="650"/>
+        <param name="width" value="650"/>
         <param name="height" value="450"/>
     </xml>
     <xml name="render_plot_matching_text">
-    	<has_text_matching expression="width = 650"/>
+        <has_text_matching expression="width = 650"/>
         <has_text_matching expression="height = 450"/>
     </xml>
     <xml name="param_counting_strategy">