--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Mar 04 10:16:47 2019 -0500
@@ -0,0 +1,1084 @@
+<macros>
+    <token name="@version@">1.4</token>
+    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@version@">scanpy</requirement>
+            <requirement type="package" version="2.0.17">loompy</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-017-1382-0</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import scanpy.api as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cat '$script_file' &&
+python '$script_file'
+    ]]>
+    </token>
+    <token name="@CMD_imports@"><![CDATA[
+import scanpy.api as sc
+import pandas as pd
+import numpy as np
+    ]]>
+    </token>
+    <xml name="inputs_anndata">
+        <conditional name="input">
+            <param name="format" type="select" label="Format for the annotated data matrix">
+                <option value="loom">loom</option>
+                <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
+            </param>
+            <when value="loom">
+                <param name="adata" type="data" format="loom" label="Annotated data matrix"/>
+                <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
+                <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
+                <param name="x_name" type="text" value="spliced" label="X_name"/>
+                <param name="obs_names" type="text" value="CellID" label="obs_names"/>
+                <param name="var_names" type="text" value="Gene" label="var_names"/>
+            </when>
+            <when value="h5ad">
+                <param name="adata" type="data" format="h5" label="Annotated data matrix"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+#if $input.format == 'loom'
+adata = sc.read_loom(
+    '$input.adata',
+    sparse=$input.sparse,
+    cleanup=$input.cleanup,
+    X_name='$input.x_name',
+    obs_names='$input.obs_names',
+    var_names='$input.var_names')
+#else if $input.format == 'h5ad'
+adata = sc.read_h5ad('$input.adata')
+#end if
+]]>
+    </token>
+    <xml name="anndata_output_format">
+        <param name="anndata_output_format" type="select" label="Format to write the annotated data matrix">
+            <option value="loom">loom</option>
+            <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
+        </param>
+    </xml>
+    <xml name="anndata_modify_output_input">
+        <conditional name="modify_anndata">
+            <param name="modify_anndata" type="select" label="Return modify annotate data matrix?">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <expand macro="anndata_output_format"/>
+            </when>
+            <when value="false"/>
+        </conditional>
+    </xml>
+    <xml name="anndata_outputs">
+        <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">
+            <filter>anndata_output_format == 'h5ad'</filter>
+        </data>
+        <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
+            <filter>anndata_output_format == 'loom'</filter>
+        </data>
+    </xml>
+    <xml name="anndata_modify_outputs">
+        <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">
+            <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'h5ad'</filter>
+        </data>
+        <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
+            <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'loom'</filter>
+        </data>
+    </xml>
+    <token name="@CMD_anndata_write_outputs@"><![CDATA[
+#if $anndata_output_format == 'loom'
+adata.write_loom('anndata.loom')
+#else if $anndata_output_format == 'h5ad'
+adata.write('anndata.h5ad')
+#end if
+]]>
+    </token>
+    <token name="@CMD_anndata_write_modify_outputs@"><![CDATA[
+#if $modify_anndata.modify_anndata == 'true'
+    #if $modify_anndata.anndata_output_format == 'loom'
+adata.write_loom('anndata.loom')
+    #elif $modify_anndata.anndata_output_format == 'h5ad'
+adata.write('anndata.h5ad')
+    #end if
+#end if
+]]>
+    </token>
+    <xml name="svd_solver">
+        <param name="svd_solver" type="select" label="SVD solver to use" help="">
+            <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>
+        </param>
+    </xml>
+    <xml name="pca_random_state">
+        <param name="random_state" type="integer" value="0" label="Initial states for the optimization" help=""/>
+    </xml>
+    <xml name="param_plot_format">
+        <param name="format" type="select" label="Format for saving figures">
+            <option value="png">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+        </param>
+    </xml>
+    <xml name="numeric_distance_metric_options">
+        <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>
+        <option value="seuclidean">seuclidean</option>
+        <option value="sqeuclidean">sqeuclidean</option>
+        <option value="wminkowski">wminkowski</option>
+    </xml>
+    <xml name="boolean_distance_metric_options">
+        <option value="dice">dice</option>
+        <option value="hamming">hamming</option>
+        <option value="jaccard">jaccard</option>
+        <option value="kulsinski">kulsinski</option>
+        <option value="rogerstanimoto">rogerstanimoto</option>
+        <option value="russellrao">russellrao</option>
+        <option value="sokalmichener">sokalmichener</option>
+        <option value="sokalsneath">sokalsneath</option>
+        <option value="yule">yule</option>
+    </xml>
+    <xml name="distance_metric_options">
+        <expand macro="numeric_distance_metric_options"/>
+        <expand macro="boolean_distance_metric_options"/>
+    </xml>
+    <xml name="seaborn_color_palette_options">
+        <option value="Accent">Accent</option>
+        <option value="Accent_r">Accent_r</option>
+        <option value="Blues">Blues</option>
+        <option value="Blues_r">Blues_r</option>
+        <option value="BrBG">BrBG</option>
+        <option value="BrBG_r">BrBG_r</option>
+        <option value="BuGn">BuGn</option>
+        <option value="BuGn_r">BuGn_r</option>
+        <option value="BuPu">BuPu</option>
+        <option value="BuPu_r">BuPu_r</option>
+        <option value="CMRmap">CMRmap</option>
+        <option value="CMRmap_r">CMRmap_r</option>
+        <option value="Dark2">Dark2</option>
+        <option value="Dark2_r">Dark2_r</option>
+        <option value="GnBu">GnBu</option>
+        <option value="GnBu_r">GnBu_r</option>
+        <option value="Greens">Greens</option>
+        <option value="Greens_r">Greens_r</option>
+        <option value="Greys">Greys</option>
+        <option value="Greys_r">Greys_r</option>
+        <option value="OrRd">OrRd</option>
+        <option value="OrRd_r">OrRd_r</option>
+        <option value="Oranges">Oranges</option>
+        <option value="Oranges_r">Oranges_r</option>
+        <option value="PRGn">PRGn</option>
+        <option value="PRGn_r">PRGn_r</option>
+        <option value="Paired">Paired</option>
+        <option value="Paired_r">Paired_r</option>
+        <option value="Pastel1">Pastel1</option>
+        <option value="Pastel1_r">Pastel1_r</option>
+        <option value="Pastel2">Pastel2</option>
+        <option value="Pastel2_r">Pastel2_r</option>
+        <option value="PiYG">PiYG</option>
+        <option value="PiYG_r">PiYG_r</option>
+        <option value="PuBu">PuBu</option>
+        <option value="PuBuGn">PuBuGn</option>
+        <option value="PuBuGn_r">PuBuGn_r</option>
+        <option value="PuBu_r">PuBu_r</option>
+        <option value="PuOr">PuOr</option>
+        <option value="PuOr_r">PuOr_r</option>
+        <option value="PuRd">PuRd</option>
+        <option value="PuRd_r">PuRd_r</option>
+        <option value="Purples">Purples</option>
+        <option value="Purples_r">Purples_r</option>
+        <option value="RdBu">RdBu</option>
+        <option value="RdBu_r">RdBu_r</option>
+        <option value="RdGy">RdGy</option>
+        <option value="RdPu">RdPu</option>
+        <option value="RdPu_r">RdPu_r</option>
+        <option value="RdYlBu">RdYlBu</option>
+        <option value="RdYlBu_r">RdYlBu_r</option>
+        <option value="RdYlGn">RdYlGn</option>
+        <option value="RdYlGn_r">RdYlGn_r</option>
+        <option value="Reds">Reds</option>
+        <option value="Reds_r">Reds_r</option>
+        <option value="Set1">Set1</option>
+        <option value="Set1_r">Set1_r</option>
+        <option value="Set2">Set2</option>
+        <option value="Set2_r">Set2_r</option>
+        <option value="Set3">Set3</option>
+        <option value="Set3_r">Set3_r</option>
+        <option value="Spectral">Spectral</option>
+        <option value="Spectral_r">Spectral_r</option>
+        <option value="Wistia">Wistia</option>
+        <option value="Wistia_r">Wistia_r</option>
+        <option value="YlGn">YlGn</option>
+        <option value="YlGn_r">YlGn_r</option>
+        <option value="YlGnBu">YlGnBu</option>
+        <option value="YlGnBu_r">YlGnBu_r</option>
+        <option value="YlOrBr">YlOrBr</option>
+        <option value="YlOrBr_r">YlOrBr_r</option>
+        <option value="YlOrRd">YlOrRd</option>
+        <option value="YlOrRd_r">YlOrRd_r</option>
+        <option value="afmhot">afmhot</option>
+        <option value="afmhot_r">afmhot_r</option>
+        <option value="autumn">autumn</option>
+        <option value="autumn_r">autumn_r</option>
+        <option value="binary">binary</option>
+        <option value="binary_r">binary_r</option>
+        <option value="bone">bone</option>
+        <option value="bone_r">bone_r</option>
+        <option value="brg">brg</option>
+        <option value="brg_r">brg_r</option>
+        <option value="bwr">bwr</option>
+        <option value="bwr_r">bwr_r</option>
+        <option value="cividis">cividis</option>
+        <option value="cividis_r">cividis_r</option>
+        <option value="cool">cool</option>
+        <option value="cool_r">cool_r</option>
+        <option value="coolwarm">coolwarm</option>
+        <option value="coolwarm_r">coolwarm_r</option>
+        <option value="copper">copper</option>
+        <option value="copper_r">copper_r</option>
+        <option value="cubehelix">cubehelix</option>
+        <option value="cubehelix_r">cubehelix_r</option>
+        <option value="flag">flag</option>
+        <option value="flag_r">flag_r</option>
+        <option value="gist_earth">gist_earth</option>
+        <option value="gist_earth_r">gist_earth_r</option>
+        <option value="gist_gray">gist_gray</option>
+        <option value="gist_gray_r">gist_gray_r</option>
+        <option value="gist_heat">gist_heat</option>
+        <option value="gist_heat_r">gist_heat_r</option>
+        <option value="gist_ncar">gist_ncar</option>
+        <option value="gist_ncar_r">gist_ncar_r</option>
+        <option value="gist_rainbow">gist_rainbow</option>
+        <option value="gist_rainbow_r">gist_rainbow_r</option>
+        <option value="gist_stern">gist_stern</option>
+        <option value="gist_stern_r">gist_stern_r</option>
+        <option value="gist_yarg">gist_yarg</option>
+        <option value="gist_yarg_r">gist_yarg_r</option>
+        <option value="gnuplot">gnuplot</option>
+        <option value="gnuplot_r">gnuplot_r</option>
+        <option value="gnuplot2">gnuplot2</option>
+        <option value="gnuplot2_r">gnuplot2_r</option>
+        <option value="gray">gray</option>
+        <option value="gray_r">gray_r</option>
+        <option value="hot">hot</option>
+        <option value="hot_r">hot_r</option>
+        <option value="hsv">hsv</option>
+        <option value="hsv_r">hsv_r</option>
+        <option value="icefire">icefire</option>
+        <option value="icefire_r">icefire_r</option>
+        <option value="inferno">inferno</option>
+        <option value="inferno_r">inferno_r</option>
+        <option value="jet">jet</option>
+        <option value="jet_r">jet_r</option>
+        <option value="magma">magma</option>
+        <option value="magma_r">magma_r</option>
+        <option value="mako">mako</option>
+        <option value="mako_r">mako_r</option>
+        <option value="nipy_spectral">nipy_spectral</option>
+        <option value="nipy_spectral_r">nipy_spectral_r</option>
+        <option value="ocean">ocean</option>
+        <option value="ocean_r">ocean_r</option>
+        <option value="pink">pink</option>
+        <option value="pink_r">pink_r</option>
+        <option value="plasma">plasma</option>
+        <option value="plasma_r">plasma_r</option>
+        <option value="prism">prism</option>
+        <option value="prism_r">prism_r</option>
+        <option value="rainbow">rainbow</option>
+        <option value="rainbow_r">rainbow_r</option>
+        <option value="rocket">rocket</option>
+        <option value="rocket_r">rocket_r</option>
+        <option value="seismic">seismic</option>
+        <option value="seismic_r">seismic_r</option>
+        <option value="spring">spring</option>
+        <option value="spring_r">spring_r</option>
+        <option value="summer">summer</option>
+        <option value="summer_r">summer_r</option>
+        <option value="tab10">tab10</option>
+        <option value="tab10_r">tab10_r</option>
+        <option value="tab20">tab20</option>
+        <option value="tab20_r">tab20_r</option>
+        <option value="tab20b">tab20b</option>
+        <option value="tab20b_r">tab20b_r</option>
+        <option value="tab20c">tab20c</option>
+        <option value="tab20c_r">tab20c_r</option>
+        <option value="terrain">terrain</option>
+        <option value="terrain_r">terrain_r</option>
+        <option value="twilight">twilight</option>
+        <option value="twilight_r">twilight_r</option>
+        <option value="twilight_shifted">twilight_shifted</option>
+        <option value="twilight_shifted_r">twilight_shifted_r</option>
+        <option value="viridis">viridis</option>
+        <option value="viridis_r">viridis_r</option>
+        <option value="vlag">vlag</option>
+        <option value="vlag_r">vlag_r</option>
+        <option value="winter">winter</option>
+        <option value="winter_r">winter_r</option>
+    </xml>
+    <xml name="matplotlib_pyplot_colormap">
+        <option value="viridis">viridis (Perceptually Uniform Sequential)</option>
+        <option value="plasma">plasma (Perceptually Uniform Sequential)</option>
+        <option value="inferno">inferno (Perceptually Uniform Sequential)</option>
+        <option value="magma">magma (Perceptually Uniform Sequential)</option>
+        <option value="cividis">cividis (Perceptually Uniform Sequential)</option>
+        <option value="Greys">Greys (Sequential)</option>
+        <option value="Purples">Purples (Sequential)</option>
+        <option value="Blues">Blues (Sequential)</option>
+        <option value="Greens">Greens (Sequential)</option>
+        <option value="Oranges">Oranges (Sequential)</option>
+        <option value="Reds">Reds (Sequential)</option>
+        <option value="YlOrBr">YlOrBr (Sequential)</option>
+        <option value="YlOrRd">YlOrRd (Sequential)</option>
+        <option value="OrRd">OrRd (Sequential)</option>
+        <option value="PuRd">PuRd (Sequential)</option>
+        <option value="RdPu">RdPu (Sequential)</option>
+        <option value="BuPu">BuPu (Sequential)</option>
+        <option value="GnBu">GnBu (Sequential)</option>
+        <option value="PuBu">PuBu (Sequential)</option>
+        <option value="YlGnBu">YlGnBu (Sequential)</option>
+        <option value="PuBuGn">PuBuGn (Sequential)</option>
+        <option value="BuGn">BuGn (Sequential)</option>
+        <option value="YlGn">YlGn (Sequential)</option>
+        <option value="binary">binary (Sequential 2)</option>
+        <option value="gist_yarg">gist_yarg (Sequential 2)</option>
+        <option value="gist_gray">gist_gray (Sequential 2)</option>
+        <option value="gray">gray (Sequential 2)</option>
+        <option value="bone">bone (Sequential 2)</option>
+        <option value="pink">pink (Sequential 2)</option>
+        <option value="spring">spring (Sequential 2)</option>
+        <option value="summer">summer (Sequential 2)</option>
+        <option value="autumn">autumn (Sequential 2)</option>
+        <option value="winter">winter (Sequential 2)</option>
+        <option value="cool">cool (Sequential 2)</option>
+        <option value="Wistia">Wistia (Sequential 2)</option>
+        <option value="hot">hot (Sequential 2)</option>
+        <option value="afmhot">afmhot (Sequential 2)</option>
+        <option value="gist_heat">gist_heat (Sequential 2)</option>
+        <option value="copper">copper (Sequential 2)</option>
+        <option value="PiYG">PiYG (Diverging)</option>
+        <option value="PRGn">PRGn (Diverging)</option>
+        <option value="BrBG">BrBG (Diverging)</option>
+        <option value="PuOr">PuOr (Diverging)</option>
+        <option value="RdGy">RdGy (Diverging)</option>
+        <option value="RdBu">RdBu (Diverging)</option>
+        <option value="RdYlBu">RdYlBu (Diverging)</option>
+        <option value="RdYlGn">RdYlGn (Diverging)</option>
+        <option value="Spectral">Spectral (Diverging)</option>
+        <option value="coolwarm">coolwarm (Diverging)</option>
+        <option value="bwr">bwr (Diverging)</option>
+        <option value="seismic">seismic (Diverging)</option>
+        <option value="twilight">twilight (Cyclic)</option>
+        <option value="twilight_shifted">twilight_shifted (Cyclic)</option>
+        <option value="hsv">hsv (Cyclic)</option>
+        <option value="Pastel1">Pastel1 (Qualitative)</option>
+        <option value="Pastel2">Pastel2 (Qualitative)</option>
+        <option value="Paired">Paired (Qualitative)</option>
+        <option value="Accent">Accent (Qualitative)</option>
+        <option value="Dark2">Dark2 (Qualitative)</option>
+        <option value="Set1">Set1 (Qualitative)</option>
+        <option value="Set2">Set2 (Qualitative)</option>
+        <option value="Set3">Set3 (Qualitative)</option>
+        <option value="tab10">tab10 (Qualitative)</option>
+        <option value="tab20">tab20 (Qualitative)</option>
+        <option value="tab20b">tab20b (Qualitative)</option>
+        <option value="tab20c">tab20c (Qualitative)</option>
+        <option value="flag">flag (Miscellaneous)</option>
+        <option value="prism">prism (Miscellaneous)</option>
+        <option value="ocean">ocean (Miscellaneous)</option>
+        <option value="gist_earth">gist_earth (Miscellaneous)</option>
+        <option value="terrain">terrain (Miscellaneous)</option>
+        <option value="gist_stern">gist_stern (Miscellaneous)</option>
+        <option value="gnuplot">gnuplot (Miscellaneous)</option>
+        <option value="gnuplot2">gnuplot2 (Miscellaneous)</option>
+        <option value="CMRmap">CMRmap (Miscellaneous)</option>
+        <option value="cubehelix">cubehelix (Miscellaneous)</option>
+        <option value="brg">brg (Miscellaneous)</option>
+        <option value="gist_rainbow">gist_rainbow (Miscellaneous)</option>
+        <option value="rainbow">rainbow (Miscellaneous)</option>
+        <option value="jet">jet (Miscellaneous)</option>
+        <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 heatmap 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`."/>
+    </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?" help=""/>
+    </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>
+            </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"/>
+            </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=""/>
+        </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`."/>
+    </xml>
+    <token name="@CMD_param_plot_inputs@"><![CDATA[
+    adata=adata,
+    save='.$format',
+    show=False,
+    ]]></token>
+    <xml name="params_plots">
+        <expand macro="pl_var_names"/>
+        <expand macro="param_groupby"/>
+        <expand macro="param_log"/>
+        <expand macro="param_use_raw"/>
+        <expand macro="param_num_categories"/>
+        <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[
+#if $method.var_names.type == 'all'
+    var_names=adata.var_names,
+#else
+    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
+    var_names=$var_names,
+#end if
+#if str($method.groupby) != ''
+    groupby='$method.groupby',
+#end if
+    log=$method.log,
+    use_raw=$method.use_raw,
+    num_categories=$method.num_categories,
+    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,
+    #else
+    var_group_positions=None,
+    var_group_labels=None,
+    #end if
+#if $method.var_group_rotation
+    var_group_rotation=$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>
+        <option value="Aqua">Aqua</option>
+        <option value="Aquamarine">Aquamarine</option>
+        <option value="Azure">Azure</option>
+        <option value="Beige">Beige</option>
+        <option value="Bisque">Bisque</option>
+        <option value="Black">Black</option>
+        <option value="BlanchedAlmond">BlanchedAlmond</option>
+        <option value="Blue">Blue</option>
+        <option value="BlueViolet">BlueViolet</option>
+        <option value="Brown">Brown</option>
+        <option value="BurlyWood">BurlyWood</option>
+        <option value="CadetBlue">CadetBlue</option>
+        <option value="Chartreuse">Chartreuse</option>
+        <option value="Chocolate">Chocolate</option>
+        <option value="Coral">Coral</option>
+        <option value="CornflowerBlue">CornflowerBlue</option>
+        <option value="Cornsilk">Cornsilk</option>
+        <option value="Crimson">Crimson</option>
+        <option value="Cyan">Cyan</option>
+        <option value="DarkBlue">DarkBlue</option>
+        <option value="DarkCyan">DarkCyan</option>
+        <option value="DarkGoldenRod">DarkGoldenRod</option>
+        <option value="DarkGray">DarkGray</option>
+        <option value="DarkGrey">DarkGrey</option>
+        <option value="DarkGreen">DarkGreen</option>
+        <option value="DarkKhaki">DarkKhaki</option>
+        <option value="DarkMagenta">DarkMagenta</option>
+        <option value="DarkOliveGreen">DarkOliveGreen</option>
+        <option value="DarkOrange">DarkOrange</option>
+        <option value="DarkOrchid">DarkOrchid</option>
+        <option value="DarkRed">DarkRed</option>
+        <option value="DarkSalmon">DarkSalmon</option>
+        <option value="DarkSeaGreen">DarkSeaGreen</option>
+        <option value="DarkSlateBlue">DarkSlateBlue</option>
+        <option value="DarkSlateGray">DarkSlateGray</option>
+        <option value="DarkSlateGrey">DarkSlateGrey</option>
+        <option value="DarkTurquoise">DarkTurquoise</option>
+        <option value="DarkViolet">DarkViolet</option>
+        <option value="DeepPink">DeepPink</option>
+        <option value="DeepSkyBlue">DeepSkyBlue</option>
+        <option value="DimGray">DimGray</option>
+        <option value="DimGrey">DimGrey</option>
+        <option value="DodgerBlue">DodgerBlue</option>
+        <option value="FireBrick">FireBrick</option>
+        <option value="FloralWhite">FloralWhite</option>
+        <option value="ForestGreen">ForestGreen</option>
+        <option value="Fuchsia">Fuchsia</option>
+        <option value="Gainsboro">Gainsboro</option>
+        <option value="GhostWhite">GhostWhite</option>
+        <option value="Gold">Gold</option>
+        <option value="GoldenRod">GoldenRod</option>
+        <option value="Gray">Gray</option>
+        <option value="Grey">Grey</option>
+        <option value="Green">Green</option>
+        <option value="GreenYellow">GreenYellow</option>
+        <option value="HoneyDew">HoneyDew</option>
+        <option value="HotPink">HotPink</option>
+        <option value="IndianRed">IndianRed</option>
+        <option value="Indigo">Indigo</option>
+        <option value="Ivory">Ivory</option>
+        <option value="Khaki">Khaki</option>
+        <option value="Lavender">Lavender</option>
+        <option value="LavenderBlush">LavenderBlush</option>
+        <option value="LawnGreen">LawnGreen</option>
+        <option value="LemonChiffon">LemonChiffon</option>
+        <option value="LightBlue">LightBlue</option>
+        <option value="LightCoral">LightCoral</option>
+        <option value="LightCyan">LightCyan</option>
+        <option value="LightGoldenRodYellow">LightGoldenRodYellow</option>
+        <option value="LightGray">LightGray</option>
+        <option value="LightGrey">LightGrey</option>
+        <option value="LightGreen">LightGreen</option>
+        <option value="LightPink">LightPink</option>
+        <option value="LightSalmon">LightSalmon</option>
+        <option value="LightSeaGreen">LightSeaGreen</option>
+        <option value="LightSkyBlue">LightSkyBlue</option>
+        <option value="LightSlateGray">LightSlateGray</option>
+        <option value="LightSlateGrey">LightSlateGrey</option>
+        <option value="LightSteelBlue">LightSteelBlue</option>
+        <option value="LightYellow">LightYellow</option>
+        <option value="Lime">Lime</option>
+        <option value="LimeGreen">LimeGreen</option>
+        <option value="Linen">Linen</option>
+        <option value="Magenta">Magenta</option>
+        <option value="Maroon">Maroon</option>
+        <option value="MediumAquaMarine">MediumAquaMarine</option>
+        <option value="MediumBlue">MediumBlue</option>
+        <option value="MediumOrchid">MediumOrchid</option>
+        <option value="MediumPurple">MediumPurple</option>
+        <option value="MediumSeaGreen">MediumSeaGreen</option>
+        <option value="MediumSlateBlue">MediumSlateBlue</option>
+        <option value="MediumSpringGreen">MediumSpringGreen</option>
+        <option value="MediumTurquoise">MediumTurquoise</option>
+        <option value="MediumVioletRed">MediumVioletRed</option>
+        <option value="MidnightBlue">MidnightBlue</option>
+        <option value="MintCream">MintCream</option>
+        <option value="MistyRose">MistyRose</option>
+        <option value="Moccasin">Moccasin</option>
+        <option value="NavajoWhite">NavajoWhite</option>
+        <option value="Navy">Navy</option>
+        <option value="OldLace">OldLace</option>
+        <option value="Olive">Olive</option>
+        <option value="OliveDrab">OliveDrab</option>
+        <option value="Orange">Orange</option>
+        <option value="OrangeRed">OrangeRed</option>
+        <option value="Orchid">Orchid</option>
+        <option value="PaleGoldenRod">PaleGoldenRod</option>
+        <option value="PaleGreen">PaleGreen</option>
+        <option value="PaleTurquoise">PaleTurquoise</option>
+        <option value="PaleVioletRed">PaleVioletRed</option>
+        <option value="PapayaWhip">PapayaWhip</option>
+        <option value="PeachPuff">PeachPuff</option>
+        <option value="Peru">Peru</option>
+        <option value="Pink">Pink</option>
+        <option value="Plum">Plum</option>
+        <option value="PowderBlue">PowderBlue</option>
+        <option value="Purple">Purple</option>
+        <option value="RebeccaPurple">RebeccaPurple</option>
+        <option value="Red">Red</option>
+        <option value="RosyBrown">RosyBrown</option>
+        <option value="RoyalBlue">RoyalBlue</option>
+        <option value="SaddleBrown">SaddleBrown</option>
+        <option value="Salmon">Salmon</option>
+        <option value="SandyBrown">SandyBrown</option>
+        <option value="SeaGreen">SeaGreen</option>
+        <option value="SeaShell">SeaShell</option>
+        <option value="Sienna">Sienna</option>
+        <option value="Silver">Silver</option>
+        <option value="SkyBlue">SkyBlue</option>
+        <option value="SlateBlue">SlateBlue</option>
+        <option value="SlateGray">SlateGray</option>
+        <option value="SlateGrey">SlateGrey</option>
+        <option value="Snow">Snow</option>
+        <option value="SpringGreen">SpringGreen</option>
+        <option value="SteelBlue">SteelBlue</option>
+        <option value="Tan">Tan</option>
+        <option value="Teal">Teal</option>
+        <option value="Thistle">Thistle</option>
+        <option value="Tomato">Tomato</option>
+        <option value="Turquoise">Turquoise</option>
+        <option value="Violet">Violet</option>
+        <option value="Wheat">Wheat</option>
+        <option value="White">White</option>
+        <option value="WhiteSmoke">WhiteSmoke</option>
+        <option value="Yellow">Yellow</option>
+        <option value="YellowGreen">YellowGreen</option>
+    </xml>
+    <xml name="param_matplotlib_pyplot_edgecolors">
+        <param argument="edgecolors" type="select" label="Edge color of the marker" help="">
+            <option value="face">The edge color will always be the same as the face color</option>
+            <option value="none">No patch boundary will be drawn</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>
+    <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
+    #if $method.matplotlib_pyplot_scatter.vmin
+    vmin=$method.matplotlib_pyplot_scatter.vmin,
+    #end if
+    #if $method.matplotlib_pyplot_scatter.vmax
+    vmax=$method.matplotlib_pyplot_scatter.vmax,
+    #end if
+    #if $method.matplotlib_pyplot_scatter.alpha
+    alpha=$method.matplotlib_pyplot_scatter.alpha,
+    #end if
+    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
+    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
+    ]]></token>
+    <xml name="section_violin_plots">
+        <section name="violin_plot" title="Violin plot attributes">
+            <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="integer" min="0" value="1" label="Size of the jitter points" help=""/>
+                        </when>
+                        <when value="False"/>
+                    </conditional>
+                </when>
+                <when value="False"/>
+            </conditional>
+            <conditional name="multi_panel">
+                <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided">
+                    <option value="True">Yes</option>
+                    <option value="False" selected="true">No</option>
+                </param>
+                <when value="True">
+                    <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
+                    <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
+                </when>
+                <when value="False"/>
+            </conditional>
+            <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>
+            </param>
+        </section>
+    </xml>
+    <token name="@CMD_params_violin_plots@"><![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
+    multi_panel=$method.violin_plot.multi_panel.multi_panel, 
+#if $method.multi_panel.violin_plot.multi_panel == "True" and $method.violin_plot.multi_panel.width and $method.violin_plot.multi_panel.height
+    figsize=($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" label="Color for all of the elements" help="">
+                <expand macro="matplotlib_color"/>
+            </param>
+            <param argument="palette" type="select" label="Colors to use for the different levels of the hue variable" help="">
+                <expand macro="matplotlib_pyplot_colormap"/>
+            </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=$method.seaborn_violinplot.linewidth,
+    color='$method.seaborn_violinplot.color',
+    palette='$method.seaborn_violinplot.palette',
+    saturation=$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`"/>
+    </xml>
+    <token name="@CMD_param_color@"><![CDATA[
+#if str($method.color) != ''
+    #set $color = ([x.strip() for x in str($method.color).split(',')])
+    color=$color,
+#else
+    color=None,
+#end if
+    ]]></token>
+    <xml name="pl_groups">
+        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/>
+    </xml>
+    <token name="@CMD_params_pl_groups@"><![CDATA[
+#if str($method.groups) != ''
+    #set $groups=([x.strip() for x in str($method.groups).split(',')])
+    groups=$groups,
+#else
+    groups=None,
+#end if
+    ]]></token>
+    <xml name="pl_components">
+        <repeat name="components" title="Component">
+            <param argument="axis1" type="text" value="1" label="Axis 1" help=""/>
+            <param argument="axis2" type="text" value="2" label="Axis 2" help=""/>
+        </repeat>
+    </xml>
+    <token name="@CMD_params_pl_components@"><![CDATA[
+#if len($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,
+#else
+    components=None,
+#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" min="0" value="1" label="Legend font size" help=""/>
+    </xml>
+    <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" label="Colors to use for plotting g categorical annotation groups" help="">
+            <expand macro="matplotlib_pyplot_colormap"/>
+        </param>
+    </xml>
+    <xml name="param_color_map">
+        <param argument="color_map" type="select" label="Colors to use for plotting categorical annotation groups" 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" value="1" label="Point size" help=""/>
+    </xml>
+    <xml name="param_title">
+        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/>
+    </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_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="Geight 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>
+            </param>
+            <when value="True">
+                <param name="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
+                <param name="edges_color" type="select" 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,
+    edges_color='$method.edges.edges_color',
+#else
+    edges=False,
+#end if
+    ]]>
+    </token>
+    <xml name="param_arrows">
+        <param name="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/>
+    </xml>
+    <xml name="param_cmap">
+        <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
+            <expand macro="matplotlib_pyplot_colormap"/>
+        </param>
+    </xml>
+    <xml name="pl_attribute_section">
+        <section name="plot" title="Plot attributes">
+            <expand macro="pl_components"/>
+            <expand macro="param_projection"/>
+            <expand macro="param_legend_loc"/>
+            <expand macro="param_legend_fontsize"/>
+            <expand macro="param_legend_fontweight"/>
+            <expand macro="param_size"/>
+            <expand macro="param_palette"/>
+            <expand macro="param_frameon"/>
+            <expand macro="param_ncols"/>
+            <expand macro="param_wspace"/>
+            <expand macro="param_hspace"/>
+            <expand macro="param_title"/>
+        </section>
+    </xml>
+    <token name="@CMD_pl_attribute_section@"><![CDATA[
+    projection='$method.plot.projection',
+    legend_loc='$method.plot.legend_loc',
+    legend_fontsize=$method.plot.legend_fontsize,
+    legend_fontweight='$method.plot.legend_fontweight',
+    size=$method.plot.size,
+    palette='$method.plot.palette',
+    frameon=$method.plot.frameon,
+    ncols=$method.plot.ncols,
+    wspace=$method.plot.wspace,
+    hspace=$method.plot.hspace,
+    #if $method.plot.title
+    title='$method.plot.title',
+    #end if
+    ]]>
+    </token>
+    <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="pl_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'."/>
+        <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."/>
+        <param argument="layout" type="select" value="" label="Plotting layout" help="">
+            <option value="fa">fa: ForceAtlas2</option>
+            <option value="fr">fr: Fruchterman-Reingold</option>
+            <option value="fr">rt: stands for Reingold Tilford</option>
+            <option value="fr">eq_tree: equally spaced tree</option>
+        </param>
+        <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=""/>
+        <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."/>
+        <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."/>
+        <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/>
+        <param argument="solid_edges" type="text" value="paga_connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for `.uns['paga']`"/>
+        <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."/>
+        <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>
+    <token name="@CMD_params_pl_paga@"><![CDATA[
+    threshold=$method.threshold,
+#if str($method.groups) != ''
+    #set $groups=([x.strip() for x in str($method.groups).split(',')])
+    groups=$groups,
+#else
+    groups=None,
+#end if
+    color='$method.color',
+#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 $method.transitions
+    transitions='$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 $method.min_edge_width
+    min_edge_width=$method.min_edge_width,
+#end if
+#if $method.max_edge_width
+    max_edge_width=$method.max_edge_width,
+#end if
+    arrowsize=$method.arrowsize,
+    normalize_to_color=$method.normalize_to_color,
+    cmap='$method.cmap',
+#if $method.title
+    title='$method.title',
+#end if
+    frameon=$method.frameon,
+    ]]>
+    </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>
+</macros>