comparison macros.xml @ 7:b2df381a6004 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"

6:77b91b9bdf52

<macros>
    <token name="@version@">1.4.4.post1</token>
    <token name="@profile@">19.01</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy2]]></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>

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')

        <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'."/>
    </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">

                <option value="all">All variables in 'adata.var_names'</option>
                <option value="custom">Subset of variables in 'adata.var_names'</option>
            </param>
            <when value="all"/>
            <when value="custom">
                <param argument="var_names" type="text" value="" label="List of variables to plot" help="They should be a valid subset of 'adata.var_names', and separated by comma"/>
            </when>
        </conditional>
    </xml>
    <xml name="param_num_categories">
        <param argument="num_categories" type="integer" min="0" value="7" label="Number of categories" help="It is only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided."/>

    </xml>
    <xml name="pl_var_group_positions">
        <repeat name="var_group_positions" title="Group of variables to highlight" help="This will draw a 'bracket' on top of the plot between the given start and end positions. If a label is given, it will be added on top of the bracket. ">
            <param name="start" type="integer" min="0" value="" label="Start" help=""/>
            <param name="end" type="integer" min="0" value="" label="End" help=""/>
            <param argument="label" type="text" value="" label="Label" help=""/>
        </repeat>
    </xml>
    <xml name="param_var_group_rotation">
        <param argument="var_group_rotation" type="float" value="" optional="true" label="Label rotation degrees" help="By default, labels larger than 4 characters are rotated 90 degrees"/>
    </xml>
    <xml name="param_layer">
        <param argument="layer" type="text" value="" label="Name of the AnnData object layer that wants to be plotted" help="By default 'adata.raw.X' is plotted. If 'use_raw=False' is set, then 'adata.X' is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over 'use_raw'."/>
    </xml>
    <token name="@CMD_param_plot_inputs@"><![CDATA[
    adata,
    save='.$format',
    show=False,

    <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>

    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>

    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=$color,
#end if
    ]]></token>
    <xml name="param_groups">
        <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"/>
    </xml>
    <token name="@CMD_params_groups@"><![CDATA[
#if str($method.groups) != ''
    #set $groups=([x.strip() for x in str($method.groups).split(',')])
    groups=$groups,
#end if
    ]]></token>
    <xml name="pl_components">
        <repeat name="components" title="Component">
            <param argument="axis1" type="text" value="1" label="X-Axis" help=""/>
            <param argument="axis2" type="text" value="2" label="Y-Axis" help=""/>
        </repeat>
    </xml>
    <token name="@CMD_params_pl_components@"><![CDATA[
#if len($method.plot.components) > 0
    #set $components=[]

            <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</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="">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=""/>

    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"/>
    </xml>
    <token name="@CMD_param_title@"><![CDATA[
    #if $method.plot.title
    title='$method.plot.title',
    #end if

    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) != ''
    color_map='$method.plot.color_map',
    #end if
    #if str($method.plot.palette) != ''
    palette='$method.plot.palette',
    #end if

        <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="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'."/>
        <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>
    <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="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">

    #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'"/>
    </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">

7:b2df381a6004

<macros>
    <token name="@version@">1.4.4.post1</token>
    <token name="@profile@">19.01</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></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>

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('anndata.h5ad')

        <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">

                <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."/>

    </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,

    <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>

    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>

    color='$method.seaborn_violinplot.color',
    palette='$method.seaborn_violinplot.palette',
    saturation=$method.seaborn_violinplot.saturation
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query" />
        </param>
    </xml>
    <token name="@CMD_param_color@"><![CDATA[
#if str($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=$groups,
#end if
    ]]></token>
    <xml name="pl_components">
        <repeat name="components" title="Component">
            <param argument="axis1" type="text" value="1" label="X-Axis" help="">
                <expand macro="sanitize_query" />
            </param>
            <param argument="axis2" type="text" value="2" label="Y-Axis" help="">
                <expand macro="sanitize_query" />
            </param>
        </repeat>
    </xml>
    <token name="@CMD_params_pl_components@"><![CDATA[
#if len($method.plot.components) > 0
    #set $components=[]

            <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=""/>

    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

    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

        <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.">
            <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=""/>

    </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=""/>
    </xml>
    <xml name="pl_dotplot">

    #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">