comparison macros.xml @ 12:1f380e8a6aec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0

11:69a12ab93cdd

<macros>
    <token name="@version@">1.7.1</token>
    <token name="@profile@">19.01</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>
            <requirement type="package" version="0.8.3">leidenalg</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">scanpy</xref>
        </xrefs>
    </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 as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>

    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read('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('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'

    <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">
                    <expand macro="sanitize_query" />
                </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."/>

        <expand macro="pl_var_names"/>
        <expand macro="param_groupby"/>
        <expand macro="param_num_categories"/>
    </xml>
    <token name="@CMD_params_inputs@"><![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='$method.groupby',
#end if
    num_categories=$method.num_categories,
    ]]></token>
    <xml name="params_plots">
        <expand macro="param_log"/>
        <expand macro="param_use_raw"/>

            #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 $method.var_group_rotation
    var_group_rotation=$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="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)"/>

            <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="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="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[
    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 $method.multi_panel.violin_plot.multi_panel == "True" and str($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',

            <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="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
        </section>
    </xml>

    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',
    saturation=$method.seaborn_violinplot.saturation
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_param_color@"><![CDATA[
#if str($method.color) != ''
    #set $color = ([x.strip() for x in str($method.color).split(',')])
    color=$color,
#end if
    ]]></token>
    <xml name="param_groups">
        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_params_groups@"><![CDATA[
#if str($method.groups) != ''
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#end if
    ]]></token>
    <xml name="pl_components">

            <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 categorical annotation groups" help="">
            <option value="default">Default</option>
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>
    </xml>
    <xml name="param_color_map">
        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
            <option value="None">Default</option>
            <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=""/>

                <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" 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 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" 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">

    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    @CMD_param_legend_fontsize@
    legend_fontweight='$method.plot.legend_fontweight',
    @CMD_param_size@
    #if str($method.plot.color_map) != 'None'
    color_map='$method.plot.color_map',
    #end if
    #if str($method.plot.palette) != ''
    palette='$method.plot.palette',
    #end if
    frameon=$method.plot.frameon,
    ncols=$method.plot.ncols,
    wspace=$method.plot.wspace,

        <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=$groups,
#end if
#if str($method.color) != ''
    #set $color=([x.strip() for x in str($method.color).split(',')])
    color=$color,
#end if
#if $method.pos
    pos=np.fromfile($method.pos, dtype=dt),
#end if
#if str($method.labels) != ''
    #set $labels=([x.strip() for x in str($method.labels).split(',')])
    labels=$labels,
#end if
    layout='$method.layout',
#if $method.init_pos
    init_pos=np.fromfile($method.init_pos, dtype=dt),
#end if
    random_state=$method.random_state,
#if str($method.root) != ''
    #set $root=([int(x.strip()) for x in str($method.root).split(',')])
    root=$root,
#end if
#if $method.transitions
    transitions='$method.transitions',

    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,
    ]]>

        <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=""/>
    </xml>
    <xml name="pl_dotplot">
        <param argument="color_map" type="select" 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[
    color_map='$method.color_map',
    #if str($method.dot_max) != ''
    dot_max=$method.dot_max,
    #end if
    #if str($method.dot_min) != ''
    dot_min=$method.dot_min,

        </section>
    </xml>
    <token name="@CMD_pl_heatmap@"><![CDATA[
    swap_axes=$method.swap_axes,
    show_gene_labels=$method.show_gene_labels,
    cmap='$method.matplotlib_pyplot_imshow.cmap',
    #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
    interpolation='$method.matplotlib_pyplot_imshow.interpolation',
    #end if
    #if $method.matplotlib_pyplot_imshow.alpha
    alpha=$method.matplotlib_pyplot_imshow.alpha,
    #end if
    #if $method.matplotlib_pyplot_imshow.vmin
    vmin=$method.matplotlib_pyplot_imshow.vmin,
    #end if
    #if $method.matplotlib_pyplot_imshow.vmax
    vmax=$method.matplotlib_pyplot_imshow.vmax,
    #end if
    origin='$method.matplotlib_pyplot_imshow.origin'
    ]]>
    </token>

        <expand macro="param_n_genes"/>
        <expand macro="param_key"/>
    </xml>
    <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
    @CMD_params_groups@
    #if str($method.n_genes) != ''
    n_genes=$method.n_genes,
    #end if
    #if str($method.key) != ''
    key='$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" 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"/>

            <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=$method.swap_axes,
    cmap='$method.matplotlib_pyplot_pcolor.cmap',
    #if $method.matplotlib_pyplot_pcolor.vmin
    vmin=$method.matplotlib_pyplot_pcolor.vmin,
    #end if
    #if $method.matplotlib_pyplot_pcolor.vmax
    vmax=$method.matplotlib_pyplot_pcolor.vmax,
    #end if
    edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
    #if $method.matplotlib_pyplot_pcolor.alpha
    alpha=$method.matplotlib_pyplot_pcolor.alpha,
    #end if
    snap=$method.matplotlib_pyplot_pcolor.snap
    ]]>
    </token>

        <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" 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>

    </xml>
    <token name="@CMD_pl_stacked_violin@"><![CDATA[
    swap_axes=$method.swap_axes,
    @CMD_conditional_stripplot@
    scale='$method.violin_plot.scale',
    row_palette='$method.row_palette',
    #if str($method.standard_scale) != 'None'
    standard_scale='$method.standard_scale',
    #end if
    @CMD_params_seaborn_violinplot@
    ]]>

12:1f380e8a6aec

<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>

    </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'

    <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>
            </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."/>

        <expand macro="pl_var_names"/>
        <expand macro="param_groupby"/>
        <expand macro="param_num_categories"/>
    </xml>
    <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"/>

            #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="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)"/>

            <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="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',

            <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>

    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">

            <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=""/>

                <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">

    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,

        <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',

    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,
    ]]>

        <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,

        </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>

        <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"/>

            <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>

        <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>

    </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@
    ]]>