Mercurial > repos > iuc > preprocess_muon

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Feb 05 10:53:25 2025 +0000
@@ -0,0 +1,264 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">muon</requirement>
+            <requirement type="package" version="0.10.2">leidenalg</requirement>
+            <requirement type="package" version="0.8.2">louvain</requirement>
+            <requirement type="package" version="0.7.2">mofapy2</requirement>
+        </requirements>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">muon</xref>
+        </xrefs>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-021-02577-8</citation>
+        </citations>
+    </xml>
+    <xml name="sanitize_query">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="sanitize_string">
+        <sanitizer>
+            <valid initial="string.letters,string.digits"><add value="_" /></valid>
+        </sanitizer>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import muon as mu;print('Muon version: %s' % mu.__version__)"]]></version_command>
+    </xml>
+
+    <token name="@CMD_imports@"><![CDATA[
+import mudata as md
+import muon as mu
+import scanpy as sc
+import os
+            ]]>
+    </token>
+    <xml name="inputs_mudata">
+        <param name="mdata" type="data" format="h5ad" label="MuData input file"/>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+mdata = md.read('mudata.h5mu')
+        ]]>
+    </token>
+    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|MuData 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="@COPY_MUDATA@"><![CDATA[
+cp '$mdata' 'mudata.h5mu' &&
+    ]]>
+    </token>
+
+    <token name="@CMD@"><![CDATA[
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+touch 'mudata_info.txt' &&
+cat 'mudata_info.txt' @CMD_prettify_stdout@
+    ]]>
+    </token>
+
+    <token name="@CMD_params_clustering@"><![CDATA[
+    #if $method.res.type == 'same'
+        #if str($method.res.resolution)
+    resolution=$method.res.resolution,
+        #end if
+    #else if $method.res.type == 'separate'
+    resolution={
+        #for $modality in $method.res.modalities
+        '$modality.mod_name': $modality.resolution,
+        #end for
+    },
+    #end if
+    #if $method.weights.type == 'same'
+        #if str($method.weights.mod_weights)
+    mod_weights=$method.weights.mod_weights,
+        #end if
+    #else if $method.weights.type == 'separate'
+    mod_weights={
+        #for $modality in $method.weights.modalities
+        '$modality.mod_name': $modality.mod_weights,
+        #end for
+    },
+    #end if
+    random_state=$method.random_state,
+    key_added='$method.key_added',
+    #if $method.neighbors_key
+    neighbors_key='$method.neighbors_key',
+    #end if
+    directed=$method.directed
+    ]]></token>
+
+    <token name="@CMD_neighbor_keys@"><![CDATA[
+    #if $method.n_keys.type == 'same'
+    neighbor_keys='$method.n_keys.neighbor_keys',
+    #else if $method.n_keys.type == 'separate'
+    neighbor_keys={
+        #for $modality in $method.n_keys.modalities
+        '$modality.mod_name': '$modality.neighbor_keys',
+        #end for
+    },
+    #end if
+    ]]></token>
+    <token name="@CMD_params_embedding@"><![CDATA[
+    #if $method.color
+    #set $color = ([x.strip() for x in str($method.color).split(',')])
+    color=$color,
+    #end if
+    use_raw=$method.use_raw,
+    #if $method.layer
+    layer='$method.layer',
+    #end if
+    ]]></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?" />
+        </section>
+    </xml>
+    <xml name="outputs_common_advanced">
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+    <xml name="muon_outputs">
+        <data name="mudata_out" format="h5ad" from_work_dir="mudata.h5mu" label="${tool.name} (${method.method}) on ${on_string}: MuData"/>
+        <expand macro="outputs_common_advanced"/>
+    </xml>
+    <token name="@CMD_mudata_write_outputs@"><![CDATA[
+mdata.write('mudata.h5mu')
+with open('mudata_info.txt','w', encoding='utf-8') as ainfo:
+    print(mdata, file=ainfo)
+        ]]>
+    </token>
+
+    <xml name="param_neighbor_keys">
+        <conditional name="n_keys">
+            <param name="type" type="select" label="Same or separate neighborhood information for each modality?">
+                <option value="same">Same neighborhood key for all modalities</option>
+                <option value="separate">Separate neighborhood keys per modality</option>
+            </param>
+            <when value="same">
+                <param argument="neighbor_keys" type="text" value="neighbors" label="Keys in .uns where per-modality neighborhood information is stored"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param argument="neighbor_keys" type="text" value="neighbors" label="Keys in .uns where neighborhood information is stored"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_resolution">
+        <conditional name="res">
+            <param name="type" type="select" label="Same or separate resolutions for each modality?">
+                <option value="same">Same resolution for all modalities</option>
+                <option value="separate">Separate resolutions per modality</option>
+            </param>
+            <when value="same">
+                <param argument="resolution" type="float" optional="true" label="Coarseness of the clustering" help="Higher values -> more clusters"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param name="resolution" type="float" label="Resolution for the above modality" help="Higher values -> more clusters"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_weight">
+        <conditional name="weights">
+            <param name="type" type="select" label="Same or separate weights for each modality?">
+                <option value="same">Same weight for all modalities</option>
+                <option value="separate">Separate weight per modality</option>
+            </param>
+            <when value="same">
+                <param argument="mod_weights" type="float" optional="true" label="Weight each modality controlling its contribution" help="Higher values -> more important"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param name="mod_weights" type="float" label="Weight for the above modality" help="Higher values -> more important"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_random_state" tokens="seed">
+        <param argument="random_state" type="integer" value="@SEED@" optional="true" label="Random seed for the optimization"/>
+    </xml>
+    <xml name="param_key_added" tokens="key_added">
+        <param argument="key_added" type="text" value="@KEY_ADDED@" label="mdata.obs key where cluster labels to be added">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_neighbors_key">
+        <param argument="neighbors_key" type="text" optional="true" label="Use neighbors connectivities as adjacency"
+        help="If not specified, look for .obsp['connectivities'] in each modality.
+        If specified, look for .obsp[.uns[neighbors_key]['connectivities_key']] in each modality for connectivities.">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_directed">
+        <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Treat the graph as directed"/>
+    </xml>
+    <xml name="param_key_added_common">
+        <param argument="key_added" type="text" optional="true" label="Key to be added to store neighbors, distances and connectivities data"
+            help="If not specified, the multimodal neighbors data is stored in .uns['neighbors'], distances and connectivities are stored in .obsp['distances'] and .obsp['connectivities'], respectively.
+            If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added + '_distances'] and connectivities in .obsp[key_added + '_connectivities'].">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_eps" tokens="eps_value">
+        <param argument="eps" type="float" value="@EPS_VALUE@" label="Small number to avoid numerical errors"/>
+    </xml>
+    <xml name="param_use_raw" tokens="label,checked">
+        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="@CHECKED@" label="@LABEL@" />
+    </xml>
+    <xml name="param_keys">
+        <conditional name="key_variables">
+            <param name="type" type="select" label="Keys to plot">
+                <option value="var_names">All variables in '.var_names'</option>
+                <option value="obs">All fields in '.obs'</option>
+                <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
+            </param>
+            <when value="var_names"/>
+            <when value="obs"/>
+            <when value="custom">
+                <param argument="keys" type="text" value="" label="Keys to plot" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
+                    <expand macro="sanitize_query" />
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_color">
+        <param argument="color" type="text" optional="true" label="Keys for variables or annotations of observations (.obs columns)" help="Can be from any modality.">
+            <expand macro="sanitize_query" />
+        </param>
+    </xml>
+    <xml name="params_embedding">
+        <expand macro="param_color"/>
+        <expand macro="param_use_raw" label="Use raw slot of AnnData as input values" checked="true"/>
+        <param argument="layer" type="text" optional="true" label="Name of the layer in the modality where a feature (from color) is derived from"
+            help="If a valid layer is provided, this takes precedence over use_raw=True">
+            <expand macro="sanitize_query" />
+        </param>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_muon.xml	Wed Feb 05 10:53:25 2025 +0000
@@ -0,0 +1,322 @@
+<tool id="preprocess_muon" name="muon filter and  normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+@COPY_MUDATA@
+@CMD@
+    ]]></command>
+    <configfiles>
+        <configfile name="script_file"><![CDATA[
+@CMD_imports@
+@CMD_read_inputs@
+
+#if $method.method == 'pp.intersect_obs'
+mu.pp.intersect_obs(
+    mdata
+)
+## Update the features. Only union features of the modalities are considered
+mdata.update_var()
+
+
+#else if $method.method == 'pp.l2norm'
+mu.pp.l2norm(
+    mdata,
+    #if $method.mod
+    mod='$method.mod',
+    #end if
+    #if $method.rep
+    rep='$method.rep',
+    #end if
+    n_pcs=$method.n_pcs,
+    copy=False
+)
+
+#else if $method.method == 'pp.neighbors'
+mu.pp.neighbors(
+    mdata,
+    #if str($method.n_neighbors)
+    n_neighbors=$method.n_neighbors,
+    #end if
+    n_bandwidth_neighbors=$method.n_bandwidth_neighbors,
+    n_multineighbors=$method.n_multineighbors,
+    @CMD_neighbor_keys@
+    metric='$method.metric',
+    #if $method.key_added
+    key_added='$method.key_added',
+    #end if
+    weight_key='$method.weight_key',
+    add_weights_to_modalities=$method.add_weights_to_modalities,
+    eps=$method.eps,
+    random_state=$method.random_state,
+    copy=False
+)
+
+#else if $method.method == 'pp.sample_obs'
+mu.pp.sample_obs(
+    mdata,
+    frac=$method.frac,
+    #if $method.groupby
+    groupby='$method.groupby',
+    #end if
+    #if str($method.min_n)
+    min_n=$method.min_n
+    #end if
+)
+#end if
+
+@CMD_mudata_write_outputs@
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="inputs_mudata"/>
+        <conditional name="method">
+            <param name="method" type="select" label="Method used for plotting">
+                    <option value="pp.intersect_obs">Subset: Subset observations present only in all modalities, using 'muon.pp.intersect_obs'</option>
+                    <option value="pp.l2norm">Normalize: Normalize observations to unit L2 norm, using 'muon.pp.l2norm'</option>
+                    <option value="pp.neighbors">Search: Multimodal nearest neighbor search, using 'muon.pp.neighbors'</option>
+                    <option value="pp.sample_obs">Return an object with some of the observations (subsampling). 'muon.pp.sample_obs'</option>
+            </param>
+            <when value="pp.intersect_obs"/>
+            <when value="pp.l2norm">
+                <param argument="mod" type="text" optional="true" label="Names of the modalities to normalize" help="Leave empty to use all modalities">
+                    <expand macro="sanitize_string" />
+                </param>
+                <param argument="rep" type="text" optional="true" label="The representation to normalize." help="X or any key for .obsm is valid, for all modalities">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="n_pcs" type="integer" min="0" value="0" label="The number of principal components to use." help="This affects the result only if a PCA representation is being normalized"/>
+            </when>
+            <when value="pp.neighbors">
+                <param argument="n_neighbors" type="integer" optional="true" label="Number of nearest neighbors to find"
+                    help="If not set, arithmetic mean of per-modality neighbors will be used"/>
+                <param argument="n_bandwidth_neighbors" type="integer" value="20" label="Number of nearest neighbors to use for bandwidth selection"/>
+                <param argument="n_multineighbors" type="integer" value="200" label="Number of nearest neighbors in each modality to consider as candidates for multimodal nearest neighbors"
+                    help="Only points in the union of per-modality nearest neighbors are candidates for multimodal nearest neighbors.
+                    This will use the same metric that was used for the nearest neighbor search in the respective modality."/>
+                <expand macro="param_neighbor_keys"/>
+                <param argument="metric" type="select" label="Distance measure to use" help="This will only be used in the final step to search for nearest neighbors in the set of candidates.">
+                    <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="dice">dice</option>
+                    <option value="hamming">hamming</option>
+                    <option value="jaccard">jaccard</option>
+                    <option value="jensenshannon">jensenshannon</option>
+                    <option value="kulsinski">kulsinski</option>
+                    <option value="mahalanobis">mahalanobis</option>
+                    <option value="matching">matching</option>
+                    <option value="minkowski">minkowski</option>
+                    <option value="rogerstanimoto">rogerstanimoto</option>
+                    <option value="russellrao">russellrao</option>
+                    <option value="seuclidean">seuclidean</option>
+                    <option value="sokalmichener">sokalmichener</option>
+                    <option value="sokalsneath">sokalsneath</option>
+                    <option value="sqeuclidean">sqeuclidean</option>
+                    <option value="wminkowski">wminkowski</option>
+                    <option value="yule">yule</option>
+                </param>
+                <expand macro="param_key_added_common"/>
+                <param argument="weight_key" type="text" value="mod_weight" label="Weight key to add to each modality’s .obs or to mdata.obs">
+                    <expand macro="sanitize_query" />
+                </param>
+                <param argument="add_weights_to_modalities" type="boolean" truevalue="True" falsevalue="False" checked="false" label="If to add weights to individual modalities" help="By default, the weights will be added to mdata.obs"/>
+                <expand macro="param_eps" eps_value="0.0001"/>
+                <expand macro="param_random_state" seed="42"/>
+            </when>
+            <when value="pp.sample_obs">
+                <param argument="frac" type="float" min="0" max="1" value="0.1" label="A fraction of observations to return"/>
+                <param argument="groupby" type="text" optional="true" label="Categorical column in .obs that is used for prior grouping before sampling observations">
+                    <expand macro="sanitize_query"/>
+                </param>
+                <param argument="min_n" type="integer" min="0" optional="true" label="Return min_n observations if fraction frac of observations is below min_n"
+                    help="When groupby is not None, min_n is applied per group."/>
+            </when>
+        </conditional>
+        <expand macro="inputs_common_advanced" />
+    </inputs>
+    <outputs>
+        <expand macro="muon_outputs"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <!-- test1: intersect_obs -->
+            <param name="mdata" ftype="h5ad" location="https://zenodo.org/records/12570984/files/pbmc3k_chr21.h5mu"/>
+            <param name="method" value="pp.intersect_obs"/>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="mu.pp.intersect_obs"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="179 × 490"/>
+                <has_text_matching expression="179 x 178"/>
+                <has_text_matching expression="179 x 312"/>
+            </assert_stdout>
+            <output name="mudata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="mod/rna"/>
+                    <has_h5_keys keys="mod/atac"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test2: l2norm -->
+            <param name="mdata" ftype="h5ad" location="https://zenodo.org/records/12570984/files/pbmc3k_chr21.h5mu"/>
+            <param name="method" value="pp.l2norm"/>
+            <param name="n_pcs" value="5"/>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="mu.pp.l2norm"/>
+                    <has_text_matching expression="copy=False"/>
+                    <has_text_matching expression="n_pcs=5"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="179 × 490"/>
+                <has_text_matching expression="179 x 178"/>
+                <has_text_matching expression="179 x 312"/>
+            </assert_stdout>
+            <output name="mudata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="mod/rna"/>
+                    <has_h5_keys keys="mod/atac"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test3: neighbors -->
+            <param name="mdata" ftype="h5ad" location="https://zenodo.org/records/12570984/files/pbmc3k_chr21_pp.neighbors_in.h5mu"/>
+            <param name="method" value="pp.neighbors"/>
+            <param name="n_neighbors" value="2"/>
+            <param name="n_bandwidth_neighbors" value="3"/>
+            <param name="n_multineighbors" value="5"/>
+            <conditional name="n_keys">
+                <param name="type" value="separate"/>
+                <repeat name="modalities">
+                    <param name="mod_name" value="rna"/>
+                    <param name="neighbor_keys" value="neighbors"/>
+                </repeat>
+                <repeat name="modalities">
+                    <param name="mod_name" value="atac"/>
+                    <param name="neighbor_keys" value="neighbors"/>
+                </repeat>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="mu.pp.neighbors"/>
+                    <has_text_matching expression="copy=False"/>
+                    <has_text_matching expression="n_neighbors=2"/>
+                    <has_text_matching expression="n_bandwidth_neighbors=3"/>
+                    <has_text_matching expression="n_multineighbors=5"/>
+                    <has_text_matching expression="metric='euclidean'"/>
+                    <has_text_matching expression="weight_key='mod_weight'"/>
+                    <has_text_matching expression="add_weights_to_modalities=False"/>
+                    <has_text_matching expression="eps=0.0001"/>
+                    <has_text_matching expression="random_state=42"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="2711 × 1781"/>
+                <has_text_matching expression="2711 x 555"/>
+                <has_text_matching expression="2711 x 1226"/>
+            </assert_stdout>
+            <output name="mudata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="mod/rna"/>
+                    <has_h5_keys keys="mod/atac"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test4: sample_obs -->
+            <param name="mdata" ftype="h5ad" location="https://zenodo.org/records/12570984/files/pbmc3k_chr21.h5mu"/>
+            <param name="method" value="pp.sample_obs"/>
+            <param name="frac" value="0.5"/>
+            <param name="min_n" value="10"/>
+            <section name="advanced_common">
+                <param name="show_log" value="true" />
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="mu.pp.sample_obs"/>
+                    <has_text_matching expression="frac=0.5"/>
+                    <has_text_matching expression="min_n=10"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text_matching expression="179 × 490"/>
+                <has_text_matching expression="179 x 178"/>
+                <has_text_matching expression="179 x 312"/>
+            </assert_stdout>
+            <output name="mudata_out" ftype="h5ad">
+                <assert_contents>
+                    <has_h5_keys keys="mod/rna"/>
+                    <has_h5_keys keys="mod/atac"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Filter: Filter observations (samples or cells) in-place using any column in .obs or in .X ('muon.pp.filter_obs')
+================================================================================================================
+
+        Filter observations (samples or cells) in-place using any column in .obs or in .X.
+
+        More details on the `muon documentation
+        <https://muon.readthedocs.io/en/latest/api/generated/muon.pp.filter_obs.html#muon.pp.filter_obs>`__
+
+Filter: Filter variables (features) ('muon.pp.filter_var')
+==========================================================
+
+        Filter variables (features, e.g. genes) in-place using any column in .var or row in .X.
+
+        More details on the `muon documentation
+        <https://muon.readthedocs.io/en/latest/api/generated/muon.pp.filter_var.html#muon.pp.filter_var>`__
+
+Subset: Subset observations (samples or cells) in-place taking observations present only in all modalities ('muon.pp.intersect_obs')
+====================================================================================================================================
+
+        Subset observations (samples or cells) in-place taking observations present only in all modalities.
+
+        More details on the `muon documentation
+        <https://muon.readthedocs.io/en/latest/api/generated/muon.pp.intersect_obs.html#muon.pp.intersect_obs>`__
+
+Normalize: Normalize observations to unit L2 norm ('muon.pp.l2norm')
+====================================================================
+
+        Normalize observations to unit L2 norm.
+
+        More details on the `muon documentation
+        <https://muon.readthedocs.io/en/latest/api/generated/muon.pp.l2norm.html#muon.pp.l2norm>`__
+
+Search: Multimodal nearest neighbor search ('muon.pp.neighbors')
+================================================================
+
+        Multimodal nearest neighbor search by implementing the multimodal nearest neighbor method of Hao et al. and Swanson et al.
+        The neighbor search efficiency on this heavily relies on UMAP. In particular, you may want to decrease
+        n_multineighbors for large data set to avoid excessive peak memory use. To achieve results as close as possible
+        to the Seurat implementation, observations must be normalized to unit L2 norm prior to running per-modality
+        nearest-neighbor search.
+
+        More details on the `muon documentation
+        <https://muon.readthedocs.io/en/latest/api/generated/muon.pp.neighbors.html#muon.pp.neighbors>`__
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file