annotate macros.xml @ 16:72a6bebab2a5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0

<macros>
    <token name="@TOOL_VERSION@">1.9.6</token>
    <token name="@VERSION_SUFFIX@">4</token>
    <token name="@profile@">21.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
            <requirement type="package" version="3.0.6">loompy</requirement>
            <requirement type="package" version="0.10.1">leidenalg</requirement>
            <requirement type="package" version="0.8.1">louvain</requirement>
            <requirement type="package" version="1.5.3">pandas</requirement>
            <requirement type="package" version="3.7">matplotlib</requirement>
            <requirement type="package" version="0.12.2">seaborn</requirement>
            <requirement type="package" version="3.0.0">magic-impute</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">scanpy</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/s13059-017-1382-0</citation>
            <citation type="doi">10.1093/gigascience/giaa102</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD@"><![CDATA[
cp '$adata' 'anndata.h5ad' &&
cat '$script_file' > '$hidden_output' &&
python '$script_file' >> '$hidden_output' &&
ls . >> '$hidden_output' &&
touch 'anndata_info.txt' &&
cat 'anndata_info.txt' @CMD_prettify_stdout@
    ]]>
    </token>
    <token name="@CMD_imports@"><![CDATA[
import scanpy as sc
import pandas as pd
import numpy as np
    ]]>
    </token>
    <xml name="sanitize_query" token_validinitial="string.printable">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <remove value="&apos;" />
            </valid>
       </sanitizer>
    </xml>
    <xml name="sanitize_vectors" token_validinitial="string.digits">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <add value=","/>
            </valid>
        </sanitizer>
    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read_h5ad('anndata.h5ad')
]]>
    </token>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Options" expanded="false">
            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
        </section>
    </xml>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
            <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write_h5ad('anndata.h5ad')
with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
    print(adata, file=ainfo)
]]>
    </token>
    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
    ]]></token>
    <xml name="svd_solver">
        <param name="svd_solver" type="select" label="SVD solver to use" help="">
            <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 plot is ordered by the respective group. It is expected that to be a categorical. If it is not a categorical observation, it would be subdivided into 'num_categories'.">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="param_use_raw">
        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/>
    </xml>
    <xml name="param_log">
        <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>
    </xml>
    <xml name="pl_figsize">
        <conditional name="figsize">
            <param name="test" type="select" label="Custom figure size" >
                <option value="yes">Yes</option>
                <option value="no" selected="true">No: the figure width is set based on the number of variable names and the height is set to 10.</option>
            </param>
            <when value="yes">
                <param argument="width" type="integer" min="0" value="10" label="Figure width" help=""/>
                <param argument="height" type="integer" min="0" value="10" label="Figure height" help=""/>
            </when>
            <when value="no"/>
        </conditional>
    </xml>
    <token name="@CMD_params_figsize@"><![CDATA[

    ]]></token>
    <xml name="pl_var_names">
        <conditional name="var_names">
            <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
                <option value="all">All variables in 'adata.var_names'</option>
                <option value="custom">Subset of variables in 'adata.var_names'</option>
                <option value="customfile">Subset of variables as a tabular file</option>
            </param>
            <when value="all"/>
            <when value="custom">
                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma">
                    <expand macro="sanitize_query" />
                </param>
            </when>
            <when value="customfile">
                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
                <param name="header" type="select" label="Header in the list of markers?">
                    <option value="included">Header incldued</option>
                    <option value="not_included">Header not included</option>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="param_num_categories">
        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>
    </xml>
    <xml name="param_dendrogram">
        <param argument="dendrogram" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Compute and plot a dendrogram?" help="groupby categories are reordered accoring to the dendrogram order. If groups of var_names are set and those groups correspond to the groupby categories, those groups are also reordered. The ‘person’ method is used to compute the pairwise correlation between categories using all var_names in raw if use_raw is None, otherwise all adata.var_names are used. The linkage method used is complete."/>
    </xml>
    <xml name="pl_var_group_positions">
        <repeat name="var_group_positions" title="Group of variables to highlight" help="This will draw a 'bracket' on top of the plot between the given start and end positions. If a label is given, it will be added on top of the bracket. ">
            <param name="start" type="integer" min="0" value="" label="Start" help=""/>
            <param name="end" type="integer" min="0" value="" label="End" help=""/>
            <param argument="label" type="text" value="" label="Label" help="">
                <expand macro="sanitize_query" />
            </param>
        </repeat>
    </xml>
    <xml name="param_var_group_rotation">
        <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>
    </xml>
    <xml name="param_layer">
        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default 'adata.raw.X' is plotted. If 'use_raw=False' is set, then 'adata.X' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over 'use_raw'.">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_param_plot_inputs@"><![CDATA[
    adata,
    save='.$format',
    show=False,
    ]]></token>
    <xml name="params_inputs">
        <expand macro="pl_var_names"/>
        <expand macro="param_groupby"/>
        <expand macro="param_num_categories"/>
    </xml>
    <token name="@CMD_var_names_header_check@"><![CDATA[
header='infer'
#if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
header=None
#end if
    ]]></token>
    <token name="@CMD_params_inputs@"><![CDATA[
    #if $method.var_names.type == 'custom'
    #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
    var_names=$var_names,
    #else if $method.var_names.type == 'customfile'
    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
    #else
    var_names=adata.var_names,
    #end if
    #if $method.groupby
    groupby='$method.groupby',
    #end if
    num_categories=$method.num_categories,
    ]]></token>
    <xml name="params_plots">
        <expand macro="param_log"/>
        <expand macro="param_use_raw"/>
        <expand macro="param_dendrogram"/>
        <expand macro="pl_var_group_positions"/>
        <expand macro="param_var_group_rotation"/>
        <expand macro="pl_figsize"/>
        <expand macro="param_layer"/>
    </xml>
    <token name="@CMD_params_plots@"><![CDATA[
    log=$method.log,
    use_raw=$method.use_raw,
    dendrogram=$method.dendrogram,
    #if len($method.var_group_positions) > 0:
        #set $var_group_positions=[]
        #set $var_group_labels=[]
        #for $i, $s in enumerate($method.var_group_positions)
            #silent $var_group_positions.append((int($s.start), int($s.end)))
            #silent $var_group_labels.append(str($s.label))
        #end for
    var_group_positions=$var_group_positions,
    var_group_labels=$var_group_labels,
    #end if
    #if str($method.var_group_rotation) != ''
        var_group_rotation=$method.var_group_rotation,
    #end if
    #if $method.figsize.test == 'yes'
        figsize=($method.figsize.width, $method.figsize.height),
    #end if
    #if $method.layer
        layer='$method.layer',
    #end if
    ]]></token>
    <xml name="matplotlib_color">
        <option value="AliceBlue">AliceBlue</option>
        <option value="AntiqueWhite">AntiqueWhite</option>
        <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" optional="true" label="Edge color of the marker" help="">
            <option value="face">The edge color will always be the same as the face color</option>
            <expand macro="matplotlib_color"/>
        </param>
    </xml>
    <xml name="param_alpha">
        <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/>
    </xml>
    <xml name="param_vmin">
        <param argument="vmin" type="float" value="" optional="true" label="Minimum value to normalize luminance data" help="If not set, it is inferred from the data and other keyword arguments"/>
    </xml>
    <xml name="param_vmax">
        <param argument="vmax" type="float" value="" optional="true" label="Maximum value to normalize luminance data" help="If not set, it is inferred from the data and other keyword arguments"/>
    </xml>
    <xml name="section_matplotlib_pyplot_scatter">
        <section name="matplotlib_pyplot_scatter" title="Parameters for matplotlib.pyplot.scatter">
            <!--<param argument="marker" type="select" label="Marker style" help="">
                <option value="o">o</option>
                <option value="v">v</option>
                <option value="^">^</option>
                <option value="8">8</option>
                <option value="s">s</option>
                <option value="p">p</option>
                <option value="*">*</option>
                <option value="h">h</option>
                <option value="H">H</option>
                <option value="D">D</option>
                <option value="d">d</option>
                <option value="P">P</option>
                <option value="X">X</option>
            </param>-->
            <expand macro="param_alpha"/>
            <expand macro="param_vmin"/>
            <expand macro="param_vmax"/>
            <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/>
            <expand macro="param_matplotlib_pyplot_edgecolors"/>
        </section>
    </xml>
    <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
    #if str($method.matplotlib_pyplot_scatter.vmin) != ''
    vmin=$method.matplotlib_pyplot_scatter.vmin,
    #end if
    #if str($method.matplotlib_pyplot_scatter.vmax) != ''
    vmax=$method.matplotlib_pyplot_scatter.vmax,
    #end if
    #if str($method.matplotlib_pyplot_scatter.alpha) != ''
    alpha=$method.matplotlib_pyplot_scatter.alpha,
    #end if
    lw=$method.matplotlib_pyplot_scatter.linewidths,
    #if $method.matplotlib_pyplot_scatter.edgecolors
    ec='$method.matplotlib_pyplot_scatter.edgecolors'
    #end if
    ]]></token>
    <xml name="conditional_stripplot">
        <conditional name="stripplot">
            <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
                <option value="True">Yes</option>
                <option value="False">No</option>
            </param>
            <when value="True">
                <conditional name="jitter">
                    <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
                        <option value="True">Yes</option>
                        <option value="False">No</option>
                    </param>
                    <when value="True">
                        <param argument="size" type="float" min="0" value="1" label="Size of the jitter points" help=""/>
                    </when>
                    <when value="False"/>
                </conditional>
            </when>
            <when value="False"/>
        </conditional>
    </xml>
    <token name="@CMD_conditional_stripplot@"><![CDATA[
    stripplot=$method.violin_plot.stripplot.stripplot,
#if $method.violin_plot.stripplot.stripplot == "True"
    jitter=$method.violin_plot.stripplot.jitter.jitter,
    #if $method.violin_plot.stripplot.jitter.jitter == "True"
    size=$method.violin_plot.stripplot.jitter.size,
    #end if
#end if
    ]]></token>
    <xml name="param_scale">
        <param argument="scale" type="select" label="Method used to scale the width of each violin">
            <option value="area">area: each violin will have the same area</option>
            <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
            <option value="width" selected="true">width: each violin will have the same width</option>
        </param>
    </xml>
    <token name="@CMD_params_violin_plots@"><![CDATA[
    @CMD_conditional_stripplot@
    multi_panel=$method.violin_plot.multi_panel.multi_panel,
#if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
    figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
#end if
    scale='$method.violin_plot.scale',
    ]]></token>
    <xml name="seaborn_violinplot">
        <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
            <param argument="bw" type="select" label="Name of a reference rule when computing the kernel bandwidth">
                <option value="scott">scott</option>
                <option value="silverman">silverman</option>
            </param>
            <param argument="orient" type="select" optional="true" label="Orientation of the plot">
                <option value="v">vertical</option>
                <option value="h">horizontal</option>
            </param>
            <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
            <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
                <expand macro="matplotlib_color"/>
            </param>
            <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
        </section>
    </xml>
    <token name="@CMD_params_seaborn_violinplot@"><![CDATA[
    bw='$method.seaborn_violinplot.bw',
#if $method.seaborn_violinplot.orient
    orient='$method.seaborn_violinplot.orient',
#end if
    linewidth=$method.seaborn_violinplot.linewidth,
    #if $method.seaborn_violinplot.color
    color='$method.seaborn_violinplot.color',
    #end if
    saturation=$method.seaborn_violinplot.saturation
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_param_color@"><![CDATA[
#if $method.color
    #set $color = ([x.strip() for x in str($method.color).split(',')])
    color=$color,
#end if
    ]]></token>
    <xml name="param_groups">
        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_params_groups@"><![CDATA[
#if $method.groups
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#end if
    ]]></token>
    <xml name="pl_components">
        <repeat name="components" title="Component">
            <param argument="axis1" type="text" value="1" label="X-Axis" help="">
                <expand macro="sanitize_query" />
            </param>
            <param argument="axis2" type="text" value="2" label="Y-Axis" help="">
                <expand macro="sanitize_query" />
            </param>
        </repeat>
    </xml>
    <token name="@CMD_params_pl_components@"><![CDATA[
#if len($method.plot.components) > 0
    #set $components=[]
    #for $i, $s in enumerate($method.plot.components)
        #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
    #end for
    components=$components,
#end if
    ]]>
    </token>
    <xml name="param_projection">
        <param argument="projection" type="select" label="Projection of plot" help="">
            <option value="2d">2d</option>
            <option value="3d">3d</option>
        </param>
    </xml>
    <xml name="param_legend_loc">
        <param argument="legend_loc" type="select" label="Location of legend" help="">
            <option value="none">none</option>
            <option value="right margin" selected="true">right margin</option>
            <option value="on data">on data</option>
            <option value="on data export">on data export</option>
            <option value="best">best</option>
            <option value="upper right">upper right</option>
            <option value="upper left">upper left</option>
            <option value="lower left">lower left</option>
            <option value="lower right">lower right</option>
            <option value="center left">center left</option>
            <option value="center right">center right</option>
            <option value="lower center">lower center</option>
            <option value="upper center">upper center</option>
            <option value="center">center</option>
        </param>
    </xml>
    <xml name="param_legend_fontsize">
        <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/>
    </xml>
    <token name="@CMD_param_legend_fontsize@"><![CDATA[
    #if str($method.plot.legend_fontsize) != ''
    legend_fontsize=$method.plot.legend_fontsize,
    #end if
    ]]>
    </token>
    <xml name="param_legend_fontweight">
        <param argument="legend_fontweight" type="select" label="Legend font weight" help="">
            <option value="light">light</option>
            <option value="normal" selected="true">normal</option>
            <option value="medium">medium</option>
            <option value="semibold">semibold</option>
            <option value="bold">bold</option>
            <option value="heavy">heavy</option>
            <option value="black">black</option>
        </param>
    </xml>
    <xml name="param_palette">
        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_color_map">
        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_frameon">
        <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
    </xml>
    <xml name="param_right_margin">
        <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel" help=""/>
    </xml>
    <xml name="param_left_margin">
        <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/>
    </xml>
    <xml name="param_size">
        <param argument="size" type="float" optional="true" value="" label="Point size" help=""/>
    </xml>
    <token name="@CMD_param_size@"><![CDATA[
    #if str($method.plot.size) != ''
    size=$method.plot.size,
    #end if
    ]]>
    </token>
    <xml name="param_title">
        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_param_title@"><![CDATA[
    #if $method.plot.title
    title='$method.plot.title',
    #end if
    ]]>
    </token>
    <xml name="param_sort_order">
        <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
    </xml>
    <xml name="param_sort_order">
        <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
    </xml>
    <xml name="param_ncols">
        <param argument="ncols" type="integer" min="0" value="4" label="Number of panels per row" help=""/>
    </xml>
    <xml name="param_wspace">
        <param argument="wspace" type="float" min="0" value="0.1" label="Width of the space between multiple panels" help=""/>
    </xml>
    <xml name="param_hspace">
        <param argument="hspace" type="float" min="0" value="0.25" label="Height of the space between multiple panels" help=""/>
    </xml>
    <xml name="pl_edges">
        <conditional name="edges">
            <param argument="edges" type="select" label="Show edges?">
                <option value="True">Yes</option>
                <option value="False" selected="true">No</option>
            </param>
            <when value="True">
                <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
                <param argument="edges_color" type="select" optional="true" label="Color of edges">
                    <expand macro="matplotlib_color"/>
                </param>
            </when>
            <when value="False"/>
        </conditional>
    </xml>
    <token name="@CMD_pl_edges@"><![CDATA[
#if str($method.edges.edges) == 'True'
    edges=True,
    edges_width=$method.edges.edges_width,
    #if $method.edges.edges_color
    edges_color='$method.edges.edges_color',
    #end if
#else
    edges=False,
#end if
    ]]>
    </token>
    <xml name="param_arrows">
        <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
    </xml>
    <xml name="param_cmap">
        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="pl_attribute_section">
        <section name="plot" title="Plot attributes">
            <expand macro="pl_components"/>
            <expand macro="param_projection"/>
            <expand macro="param_legend_loc"/>
            <expand macro="param_legend_fontsize"/>
            <expand macro="param_legend_fontweight"/>
            <expand macro="param_size"/>
            <expand macro="param_color_map"/>
            <expand macro="param_palette"/>
            <expand macro="param_frameon"/>
            <expand macro="param_ncols"/>
            <expand macro="param_wspace"/>
            <expand macro="param_hspace"/>
            <expand macro="param_title"/>
        </section>
    </xml>
    <token name="@CMD_pl_attribute_section@"><![CDATA[
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    @CMD_param_legend_fontsize@
    legend_fontweight='$method.plot.legend_fontweight',
    @CMD_param_size@
    #if $method.plot.color_map
    color_map='$method.plot.color_map',
    #end if
    #if $method.plot.palette
    palette='$method.plot.palette',
    #end if
    frameon=$method.plot.frameon,
    ncols=$method.plot.ncols,
    wspace=$method.plot.wspace,
    hspace=$method.plot.hspace,
    @CMD_param_title@
    ]]>
    </token>
    <xml name="options_layout">
        <option value="fa">fa: ForceAtlas2</option>
        <option value="fr">fr: Fruchterman-Reingold</option>
        <option value="grid_fr">grid_fr: Grid Fruchterman Reingold, faster than "fr"</option>
        <option value="kk">kk: Kamadi Kawai’, slower than "fr"</option>
        <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
        <option value="rt">rt: Reingold Tilford tree layout</option>
        <option value="eq_tree">eq_tree: Equally spaced tree</option>
    </xml>
    <xml name="param_layout">
        <param argument="layout" type="select" label="Plotting layout" optional="false" help="">
            <expand macro="options_layout"/>
        </param>
    </xml>
    <xml name="param_root">
        <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="param_random_state">
        <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/>
    </xml>
    <xml name="inputs_paga">
        <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
        <expand macro="param_groups"/>
        <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'.">
            <expand macro="sanitize_query" />
        </param>
        <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/>
        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed.">
            <expand macro="sanitize_query" />
        </param>
        <expand macro="param_layout"/>
        <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/>
        <expand macro="param_random_state"/>
        <expand macro="param_root"/>
        <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'">
            <expand macro="sanitize_query" />
        </param>
        <param argument="solid_edges" type="text" value="connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for uns/paga">
            <expand macro="sanitize_query" />
        </param>
        <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn.">
            <expand macro="sanitize_query" />
        </param>
        <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
        <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
        <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
        <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/>
        <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>
        <param argument="min_edge_width" type="float" min="0" value="" optional="true" label="Min width of solid edges" help=""/>
        <param argument="max_edge_width" type="float" min="0" value="" optional="true" label="Max width of solid and dashed edges" help=""/>
        <param argument="arrowsize" type="integer" min="0" value="30" label="Arrow size" help="For directed graphs, choose the size of the arrow head head's length and width."/>
        <param argument="normalize_to_color" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Normalize categorical plots to color or the underlying grouping?" help=""/>
        <expand macro="param_cmap"/>
        <expand macro="param_title"/>
        <expand macro="param_frameon"/>
    </xml>
    <token name="@CMD_params_pl_paga@"><![CDATA[
    threshold=$method.threshold,
#if $method.groups
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#end if
#if $method.color
    #set $color=([x.strip() for x in str($method.color).split(',')])
    color=$color,
#end if
#if $method.pos
    pos=np.fromfile($method.pos, dtype=dt),
#end if
#if $method.labels
    #set $labels=([x.strip() for x in str($method.labels).split(',')])
    labels=$labels,
#end if
    layout='$method.layout',
#if $method.init_pos
    init_pos=np.fromfile($method.init_pos, dtype=dt),
#end if
    random_state=$method.random_state,
#if $method.root
    #set $root=([int(x.strip()) for x in str($method.root).split(',')])
    root=$root,
#end if
#if $method.transitions
    transitions='$method.transitions',
#end if
    solid_edges='$method.solid_edges',
#if $method.dashed_edges
    dashed_edges='$method.dashed_edges',
#end if
    single_component=$method.single_component,
    fontsize=$method.fontsize,
    node_size_scale=$method.node_size_scale,
    node_size_power=$method.node_size_power,
    edge_width_scale=$method.edge_width_scale,
#if str($method.min_edge_width) != ''
    min_edge_width=$method.min_edge_width,
#end if
#if str($method.max_edge_width) != ''
    max_edge_width=$method.max_edge_width,
#end if
    arrowsize=$method.arrowsize,
    normalize_to_color=$method.normalize_to_color,
    #if $method.cmap
    cmap='$method.cmap',
    #end if
#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>
    <xml name="gene_symbols">
        <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="param_n_genes">
        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
    </xml>
    <xml name="pl_dotplot">
        <param argument="color_map" type="select" optional="true" label="Color palette">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
        <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
        <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
        <expand macro="section_matplotlib_pyplot_scatter"/>
    </xml>
    <token name="@CMD_pl_dotplot@"><![CDATA[
    #if $method.color_map
    color_map='$method.color_map',
    #end if
    #if str($method.dot_max) != ''
    dot_max=$method.dot_max,
    #end if
    #if str($method.dot_min) != ''
    dot_min=$method.dot_min,
    #end if
    @CMD_params_matplotlib_pyplot_scatter@
    ]]>
    </token>
    <xml name="param_key">
        <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <xml name="pl_heatmap">
        <expand macro="param_swap_axes"/>
        <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/>
        <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
            <expand macro="param_cmap"/>
            <param name="interpolation" type="select" label="Interpolation method" help="">
                <option value="None">none</option>
                <option value="nearest">nearest</option>
                <option value="bilinear">bilinear</option>
                <option value="bicubic">bicubic</option>
                <option value="spline16">spline16</option>
                <option value="spline36">spline36</option>
                <option value="hanning">hanning</option>
                <option value="hamming">hamming</option>
                <option value="hermite">hermite</option>
                <option value="kaiser">kaiser</option>
                <option value="quadric">quadric</option>
                <option value="catrom">catrom</option>
                <option value="gaussian">gaussian</option>
                <option value="bessel">bessel</option>
                <option value="sinc">sinc</option>
                <option value="mitchell">mitchell</option>
                <option value="lanczos">lanczos</option>
            </param>
            <expand macro="param_alpha"/>
            <expand macro="param_vmin"/>
            <expand macro="param_vmax"/>
            <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">
                <option value="upper">Upper</option>
                <option value="lower">Lower</option>
            </param>
        </section>
    </xml>
    <token name="@CMD_pl_heatmap@"><![CDATA[
    swap_axes=$method.swap_axes,
    show_gene_labels=$method.show_gene_labels,
    #if $method.matplotlib_pyplot_imshow.cmap
    cmap='$method.matplotlib_pyplot_imshow.cmap',
    #end if
    #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
    interpolation='$method.matplotlib_pyplot_imshow.interpolation',
    #end if
    #if str($method.matplotlib_pyplot_imshow.alpha) != ''
    alpha=$method.matplotlib_pyplot_imshow.alpha,
    #end if
    #if str($method.matplotlib_pyplot_imshow.vmin) != ''
    vmin=$method.matplotlib_pyplot_imshow.vmin,
    #end if
    #if str($method.matplotlib_pyplot_imshow.vmax) != ''
    vmax=$method.matplotlib_pyplot_imshow.vmax,
    #end if
    origin='$method.matplotlib_pyplot_imshow.origin'
    ]]>
    </token>
    <xml name="pl_rank_genes_groups_ext">
        <expand macro="param_groups"/>
        <expand macro="param_n_genes"/>
        <expand macro="param_key"/>
    </xml>
    <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
    @CMD_params_groups@
    n_genes=$method.n_genes,
    #if $method.key
    key='$method.key',
    #end if
    ]]>
    </token>
    <xml name="pl_matrixplot">
        <expand macro="param_swap_axes"/>
        <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
            <param argument="cmap" type="select" optional="true" label="Color palette">
                <expand macro="seaborn_color_palette_options"/>
            </param>
            <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
            <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
            <expand macro="param_matplotlib_pyplot_edgecolors"/>
            <expand macro="param_alpha"/>
            <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
        </section>
    </xml>
    <token name="@CMD_pl_matrixplot@"><![CDATA[
    swap_axes=$method.swap_axes,
    #if $method.matplotlib_pyplot_pcolor.cmap
    cmap='$method.matplotlib_pyplot_pcolor.cmap',
    #end if
    #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
    vmin=$method.matplotlib_pyplot_pcolor.vmin,
    #end if
    #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
    vmax=$method.matplotlib_pyplot_pcolor.vmax,
    #end if
    #if $method.matplotlib_pyplot_pcolor.edgecolors
    ec='$method.matplotlib_pyplot_pcolor.edgecolors',
    #end if
    #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
    alpha=$method.matplotlib_pyplot_pcolor.alpha,
    #end if
    snap=$method.matplotlib_pyplot_pcolor.snap
    ]]>
    </token>
    <xml name="pl_stacked_violin">
        <expand macro="param_swap_axes"/>
        <section name="violin_plot" title="Violin plot attributes">
            <expand macro="conditional_stripplot"/>
            <expand macro="param_scale"/>
        </section>
        <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
            <option value="muted">muted</option>
            <expand macro="seaborn_color_palette_options"/>
        </param>
        <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
            <option value="None">No standardization</option>
            <option value="var">Standardization on variable</option>
            <option value="obs">Standardization on observation</option>
        </param>
        <expand macro="seaborn_violinplot"/>
    </xml>
    <token name="@CMD_pl_stacked_violin@"><![CDATA[
    swap_axes=$method.swap_axes,
    @CMD_conditional_stripplot@
    scale='$method.violin_plot.scale',
    #if $method.row_palette
    row_palette='$method.row_palette',
    #end if
    #if str($method.standard_scale) != 'None'
    standard_scale='$method.standard_scale',
    #end if
    @CMD_params_seaborn_violinplot@
    ]]>
    </token>
</macros>