comparison macros.xml @ 1:a89ee42625ad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"

0:9ca360dde8e3

<macros>
    <token name="@version@">1.4</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="2.0.17">loompy</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy.api as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD@"><![CDATA[
cat '$script_file' &&
python '$script_file'
    ]]>
    </token>
    <token name="@CMD_imports@"><![CDATA[
import scanpy.api as sc
import pandas as pd
import numpy as np
    ]]>
    </token>
    <xml name="inputs_anndata">
        <conditional name="input">
            <param name="format" type="select" label="Format for the annotated data matrix">
                <option value="loom">loom</option>
                <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
            </param>
            <when value="loom">
                <param name="adata" type="data" format="loom" label="Annotated data matrix"/>
                <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
                <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
                <param name="x_name" type="text" value="spliced" label="X_name"/>
                <param name="obs_names" type="text" value="CellID" label="obs_names"/>
                <param name="var_names" type="text" value="Gene" label="var_names"/>
            </when>
            <when value="h5ad">
                <param name="adata" type="data" format="h5" label="Annotated data matrix"/>
            </when>
        </conditional>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
#if $input.format == 'loom'
adata = sc.read_loom(
    '$input.adata',
    sparse=$input.sparse,
    cleanup=$input.cleanup,
    X_name='$input.x_name',
    obs_names='$input.obs_names',
    var_names='$input.var_names')
#else if $input.format == 'h5ad'
adata = sc.read_h5ad('$input.adata')
#end if
]]>
    </token>
    <xml name="anndata_output_format">
        <param name="anndata_output_format" type="select" label="Format to write the annotated data matrix">
            <option value="loom">loom</option>
            <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
        </param>
    </xml>
    <xml name="anndata_modify_output_input">
        <conditional name="modify_anndata">
            <param name="modify_anndata" type="select" label="Return modify annotate data matrix?">
                <option value="true">Yes</option>
                <option value="false">No</option>
            </param>
            <when value="true">
                <expand macro="anndata_output_format"/>
            </when>
            <when value="false"/>
        </conditional>
    </xml>
    <xml name="anndata_outputs">
        <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">
            <filter>anndata_output_format == 'h5ad'</filter>
        </data>
        <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
            <filter>anndata_output_format == 'loom'</filter>
        </data>
    </xml>
    <xml name="anndata_modify_outputs">
        <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">
            <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'h5ad'</filter>
        </data>
        <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
            <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'loom'</filter>
        </data>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
#if $anndata_output_format == 'loom'
adata.write_loom('anndata.loom')
#else if $anndata_output_format == 'h5ad'
adata.write('anndata.h5ad')
#end if
]]>
    </token>
    <token name="@CMD_anndata_write_modify_outputs@"><![CDATA[
#if $modify_anndata.modify_anndata == 'true'
    #if $modify_anndata.anndata_output_format == 'loom'
adata.write_loom('anndata.loom')
    #elif $modify_anndata.anndata_output_format == 'h5ad'
adata.write('anndata.h5ad')
    #end if
#end if
]]>
    </token>
    <xml name="svd_solver">
        <param name="svd_solver" type="select" label="SVD solver to use" help="">
            <option value="auto">Automatically chosen depending on the size of the problem</option>

    </xml>
    <xml name="param_use_raw">
        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/>
    </xml>
    <xml name="param_log">
        <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?" help=""/>
    </xml>
    <xml name="pl_figsize">
        <conditional name="figsize">
            <param name="test" type="select" label="Custom figure size" >
                <option value="yes">Yes</option>

    </xml>
    <xml name="param_layer">
        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/>
    </xml>
    <token name="@CMD_param_plot_inputs@"><![CDATA[
    adata=adata,
    save='.$format',
    show=False,
    ]]></token>
    <xml name="params_plots">
        <expand macro="pl_var_names"/>

            #silent $var_group_positions.append((int($s.start), int($s.end)))
            #silent $var_group_labels.append(str($s.label))
        #end for
    var_group_positions=$var_group_positions,
    var_group_labels=$var_group_labels,
    #else
    var_group_positions=None,
    var_group_labels=None,
    #end if
#if $method.var_group_rotation
    var_group_rotation=$method.var_group_rotation,
#end if
#if $method.figsize.test == 'yes'

    alpha=$method.matplotlib_pyplot_scatter.alpha,
    #end if
    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
    ]]></token>
    <xml name="section_violin_plots">
        <section name="violin_plot" title="Violin plot attributes">
            <conditional name="stripplot">
                <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
                    <option value="True">Yes</option>
                    <option value="False">No</option>
                </param>
                <when value="True">
                    <conditional name="jitter">
                        <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
                            <option value="True">Yes</option>
                            <option value="False">No</option>
                        </param>
                        <when value="True">
                            <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/>
                        </when>
                        <when value="False"/>
                    </conditional>
                </when>
                <when value="False"/>
            </conditional>
            <conditional name="multi_panel">
                <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided">
                    <option value="True">Yes</option>
                    <option value="False" selected="true">No</option>
                </param>
                <when value="True">
                    <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
                    <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
                </when>
                <when value="False"/>
            </conditional>
            <param argument="scale" type="select" label="Method used to scale the width of each violin">
                <option value="area">area: each violin will have the same area</option>
                <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
                <option value="width" selected="true">width: each violin will have the same width</option>
            </param>
        </section>
    </xml>
    <token name="@CMD_params_violin_plots@"><![CDATA[
    stripplot=$method.violin_plot.stripplot.stripplot,
#if $method.violin_plot.stripplot.stripplot == "True"
    jitter=$method.violin_plot.stripplot.jitter.jitter,
    #if $method.violin_plot.stripplot.jitter.jitter == "True"
    size=$method.violin_plot.stripplot.jitter.size,
    #end if
#end if
    multi_panel=$method.violin_plot.multi_panel.multi_panel, 
#if $method.multi_panel.violin_plot.multi_panel == "True" and $method.violin_plot.multi_panel.width and $method.violin_plot.multi_panel.height
    figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
#end if
    scale='$method.violin_plot.scale',
    ]]></token>
    <xml name="seaborn_violinplot">

    color='$method.seaborn_violinplot.color',
    palette='$method.seaborn_violinplot.palette',
    saturation=$method.seaborn_violinplot.saturation,
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes`" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/>
    </xml>
    <token name="@CMD_param_color@"><![CDATA[
#if str($method.color) != ''
    #set $color = ([x.strip() for x in str($method.color).split(',')])
    color=$color,
#else
    color=None,
#end if
    ]]></token>
    <xml name="pl_groups">
        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/>
    </xml>
    <token name="@CMD_params_pl_groups@"><![CDATA[
#if str($method.groups) != ''
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#else
    groups=None,
#end if
    ]]></token>
    <xml name="pl_components">
        <repeat name="components" title="Component">
            <param argument="axis1" type="text" value="1" label="Axis 1" help=""/>

    #set $components=[]
    #for $i, $s in enumerate($method.plot.components)
        #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
    #end for
    components=$components,
#else
    components=None,
#end if
    ]]>
    </token>
    <xml name="param_projection">
        <param argument="projection" type="select" label="Projection of plot" help="">

            <option value="upper center">upper center</option>
            <option value="center">center</option>
        </param>
    </xml>
    <xml name="param_legend_fontsize">
        <param argument="legend_fontsize" type="integer" min="0" value="1" label="Legend font size" help=""/>
    </xml>
    <xml name="param_legend_fontweight">
        <param argument="legend_fontweight" type="select" label="Legend font weight" help="">
            <option value="light">light</option>
            <option value="normal" selected="true">normal</option>

    </xml>
    <xml name="param_left_margin">
        <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/>
    </xml>
    <xml name="param_size">
        <param argument="size" type="float" value="1" label="Point size" help=""/>
    </xml>
    <xml name="param_title">
        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/>
    </xml>
    <xml name="param_sort_order">

            <param argument="edges" type="select" label="Show edges?">
                <option value="True">Yes</option>
                <option value="False" selected="true">No</option>
            </param>
            <when value="True">
                <param name="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
                <param name="edges_color" type="select" label="Color of edges">
                    <expand macro="matplotlib_color"/>
                </param>
            </when>
            <when value="False"/>
        </conditional>

    edges=False,
#end if
    ]]>
    </token>
    <xml name="param_arrows">
        <param name="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/>
    </xml>
    <xml name="param_cmap">
        <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
            <expand macro="matplotlib_pyplot_colormap"/>
        </param>

        </section>
    </xml>
    <token name="@CMD_pl_attribute_section@"><![CDATA[
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    legend_fontsize=$method.plot.legend_fontsize,
    legend_fontweight='$method.plot.legend_fontweight',
    size=$method.plot.size,
    palette='$method.plot.palette',
    frameon=$method.plot.frameon,
    ncols=$method.plot.ncols,
    wspace=$method.plot.wspace,
    hspace=$method.plot.hspace,
    #if $method.plot.title
    title='$method.plot.title',
    #end if
    ]]>
    </token>
    <xml name="inputs_paga">
        <param argument="threshold" type="float" min="0" value="0.01" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
        <expand macro="pl_groups"/>
        <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."/>
        <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/>
        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which `tl.paga` has been computed."/>
        <param argument="layout" type="select" value="" label="Plotting layout" help="">
            <option value="fa">fa: ForceAtlas2</option>
            <option value="fr">fr: Fruchterman-Reingold</option>
            <option value="fr">rt: stands for Reingold Tilford</option>
            <option value="fr">eq_tree: equally spaced tree</option>
        </param>
        <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout" help=""/>
        <param argument="random_state" type="integer" value="0" label="Random state" help="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If `None`, the initial state is not reproducible."/>
        <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting."/>
        <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/>
        <param argument="solid_edges" type="text" value="paga_connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for `.uns['paga']`"/>
        <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for `.uns['paga']`. If not set, no dashed edges are drawn."/>
        <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
        <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
        <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
        <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/>
        <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>

    <token name="@CMD_params_pl_paga@"><![CDATA[
    threshold=$method.threshold,
#if str($method.groups) != ''
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#else
    groups=None,
#end if
    color='$method.color',
#if $method.pos
    pos=np.fromfile($method.pos, dtype=dt),
#end if
#if str($method.labels) != ''
    #set $labels=([x.strip() for x in str($method.labels).split(',')])

    ]]>
    </token>
    <xml name="param_swap_axes">
        <param argument="swap_axes" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Swap axes?" help="By default, the x axis contains `var_names` (e.g. genes) and the y axis the `groupby` categories (if any). By setting `swap_axes` then x are the `groupby` categories and y the `var_names`."/>
    </xml>
</macros>

1:a89ee42625ad

<macros>
    <token name="@version@">1.4.4</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="2.0.17">loompy</requirement>
            <requirement type="package" version="2.9.0">h5py</requirement>
            <requirement type="package" version="0.7.0">leidenalg</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13059-017-1382-0</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD@"><![CDATA[
cp '$adata' 'anndata.h5ad' &&
cat '$script_file' &&
python '$script_file' &&
ls .
    ]]>
    </token>
    <token name="@CMD_imports@"><![CDATA[
import scanpy as sc
import pandas as pd
import numpy as np
    ]]>
    </token>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read('anndata.h5ad')
]]>
    </token>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write('anndata.h5ad')
]]>
    </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>

    </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>

    </xml>
    <xml name="param_layer">
        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default `adata.raw.X` is plotted. If `use_raw=False` is set, then `adata.X` is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over `use_raw`."/>
    </xml>
    <token name="@CMD_param_plot_inputs@"><![CDATA[
    adata,
    save='.$format',
    show=False,
    ]]></token>
    <xml name="params_plots">
        <expand macro="pl_var_names"/>

            #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 $method.var_group_rotation
    var_group_rotation=$method.var_group_rotation,
#end if
#if $method.figsize.test == 'yes'

    alpha=$method.matplotlib_pyplot_scatter.alpha,
    #end if
    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
    ]]></token>
    <xml name="conditional_stripplot">
        <conditional name="stripplot">
            <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
                <option value="True">Yes</option>
                <option value="False">No</option>
            </param>
            <when value="True">
                <conditional name="jitter">
                    <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
                        <option value="True">Yes</option>
                        <option value="False">No</option>
                    </param>
                    <when value="True">
                        <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/>
                    </when>
                    <when value="False"/>
                </conditional>
            </when>
            <when value="False"/>
        </conditional>
    </xml>
    <token name="@CMD_conditional_stripplot@"><![CDATA[
    stripplot=$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[
    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',
    ]]></token>
    <xml name="seaborn_violinplot">

    color='$method.seaborn_violinplot.color',
    palette='$method.seaborn_violinplot.palette',
    saturation=$method.seaborn_violinplot.saturation,
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/>
    </xml>
    <token name="@CMD_param_color@"><![CDATA[
#if str($method.color) != ''
    #set $color = ([x.strip() for x in str($method.color).split(',')])
    color=$color,
#end if
    ]]></token>
    <xml name="pl_groups">
        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/>
    </xml>
    <token name="@CMD_params_pl_groups@"><![CDATA[
#if str($method.groups) != ''
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#end if
    ]]></token>
    <xml name="pl_components">
        <repeat name="components" title="Component">
            <param argument="axis1" type="text" value="1" label="Axis 1" help=""/>

    #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="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>
    <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>

    </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>
    <xml name="param_title">
        <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/>
    </xml>
    <xml name="param_sort_order">

            <param argument="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" label="Color of edges">
                    <expand macro="matplotlib_color"/>
                </param>
            </when>
            <when value="False"/>
        </conditional>

    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>

        </section>
    </xml>
    <token name="@CMD_pl_attribute_section@"><![CDATA[
    projection='$method.plot.projection',
    legend_loc='$method.plot.legend_loc',
    #if str($method.plot.legend_fontsize) != ''
    legend_fontsize=$method.plot.legend_fontsize,
    #end if
    legend_fontweight='$method.plot.legend_fontweight',
    #if str($method.plot.size) != ''
    size=$method.plot.size,
    #end if
    palette='$method.plot.palette',
    frameon=$method.plot.frameon,
    ncols=$method.plot.ncols,
    wspace=$method.plot.wspace,
    hspace=$method.plot.hspace,
    #if $method.plot.title
    title='$method.plot.title',
    #end if
    ]]>
    </token>
    <xml name="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" 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."/>
    </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="pl_groups"/>
        <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."/>
        <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing" help=""/>
        <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which `tl.paga` has been computed."/>
        <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'"/>
        <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"/>
        <param argument="dashed_edges" type="text" value="" optional="true" label="Key corresponding to the matrix storing the edges to be drawn dashed grey" help="Key for uns/paga. If not set, no dashed edges are drawn."/>
        <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
        <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
        <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
        <param argument="node_size_power" type="float" min="0" value="0.5" label="Power with which groups sizes influence the radius of the nodes" help=""/>
        <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>

    <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(',')])

    ]]>
    </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"/>
    </xml>
    <xml name="n_genes">
        <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/>
    </xml>               
</macros>