comparison macros.xml @ 7:a407e7f8bdc1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 16:09:36 -0400
parents 3bcd5445cd7a
children 5342ce58cd1e
comparison
equal deleted inserted replaced
6:3bcd5445cd7a 7:a407e7f8bdc1
1 <macros> 1 <macros>
2 <token name="@version@">1.4.4.post1</token> 2 <token name="@version@">1.4.4.post1</token>
3 <token name="@profile@">19.01</token> 3 <token name="@profile@">19.01</token>
4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy2]]></token> 4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@version@">scanpy</requirement> 7 <requirement type="package" version="@version@">scanpy</requirement>
8 <requirement type="package" version="2.0.17">loompy</requirement> 8 <requirement type="package" version="2.0.17">loompy</requirement>
9 <requirement type="package" version="2.9.0">h5py</requirement> 9 <requirement type="package" version="2.9.0">h5py</requirement>
35 import scanpy as sc 35 import scanpy as sc
36 import pandas as pd 36 import pandas as pd
37 import numpy as np 37 import numpy as np
38 ]]> 38 ]]>
39 </token> 39 </token>
40 <xml name="sanitize_query" token_validinitial="string.printable">
41 <sanitizer>
42 <valid initial="@VALIDINITIAL@">
43 <remove value="&apos;" />
44 </valid>
45 </sanitizer>
46 </xml>
47 <xml name="sanitize_vectors" token_validinitial="string.digits">
48 <sanitizer>
49 <valid initial="@VALIDINITIAL@">
50 <add value=","/>
51 </valid>
52 </sanitizer>
53 </xml>
40 <xml name="inputs_anndata"> 54 <xml name="inputs_anndata">
41 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> 55 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
42 </xml> 56 </xml>
43 <token name="@CMD_read_inputs@"><![CDATA[ 57 <token name="@CMD_read_inputs@"><![CDATA[
44 adata = sc.read('anndata.h5ad') 58 adata = sc.read('anndata.h5ad')
366 <option value="jet">jet (Miscellaneous)</option> 380 <option value="jet">jet (Miscellaneous)</option>
367 <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option> 381 <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option>
368 <option value="gist_ncar">gist_ncar (Miscellaneous)</option> 382 <option value="gist_ncar">gist_ncar (Miscellaneous)</option>
369 </xml> 383 </xml>
370 <xml name="param_groupby"> 384 <xml name="param_groupby">
371 <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'."/> 385 <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'.">
386 <expand macro="sanitize_query" />
387 </param>
372 </xml> 388 </xml>
373 <xml name="param_use_raw"> 389 <xml name="param_use_raw">
374 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/> 390 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/>
375 </xml> 391 </xml>
376 <xml name="param_log"> 392 <xml name="param_log">
398 <option value="all">All variables in 'adata.var_names'</option> 414 <option value="all">All variables in 'adata.var_names'</option>
399 <option value="custom">Subset of variables in 'adata.var_names'</option> 415 <option value="custom">Subset of variables in 'adata.var_names'</option>
400 </param> 416 </param>
401 <when value="all"/> 417 <when value="all"/>
402 <when value="custom"> 418 <when value="custom">
403 <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"/> 419 <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">
420 <expand macro="sanitize_query" />
421 </param>
404 </when> 422 </when>
405 </conditional> 423 </conditional>
406 </xml> 424 </xml>
407 <xml name="param_num_categories"> 425 <xml name="param_num_categories">
408 <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."/> 426 <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."/>
412 </xml> 430 </xml>
413 <xml name="pl_var_group_positions"> 431 <xml name="pl_var_group_positions">
414 <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. "> 432 <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. ">
415 <param name="start" type="integer" min="0" value="" label="Start" help=""/> 433 <param name="start" type="integer" min="0" value="" label="Start" help=""/>
416 <param name="end" type="integer" min="0" value="" label="End" help=""/> 434 <param name="end" type="integer" min="0" value="" label="End" help=""/>
417 <param argument="label" type="text" value="" label="Label" help=""/> 435 <param argument="label" type="text" value="" label="Label" help="">
436 <expand macro="sanitize_query" />
437 </param>
418 </repeat> 438 </repeat>
419 </xml> 439 </xml>
420 <xml name="param_var_group_rotation"> 440 <xml name="param_var_group_rotation">
421 <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"/> 441 <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"/>
422 </xml> 442 </xml>
423 <xml name="param_layer"> 443 <xml name="param_layer">
424 <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'."/> 444 <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'.">
445 <expand macro="sanitize_query" />
446 </param>
425 </xml> 447 </xml>
426 <token name="@CMD_param_plot_inputs@"><![CDATA[ 448 <token name="@CMD_param_plot_inputs@"><![CDATA[
427 adata, 449 adata,
428 save='.$format', 450 save='.$format',
429 show=False, 451 show=False,
641 <xml name="param_vmin"> 663 <xml name="param_vmin">
642 <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"/> 664 <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"/>
643 </xml> 665 </xml>
644 <xml name="param_vmax"> 666 <xml name="param_vmax">
645 <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"/> 667 <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"/>
646 </xml> 668 </xml>
647 <xml name="section_matplotlib_pyplot_scatter"> 669 <xml name="section_matplotlib_pyplot_scatter">
648 <section name="matplotlib_pyplot_scatter" title="Parameters for matplotlib.pyplot.scatter"> 670 <section name="matplotlib_pyplot_scatter" title="Parameters for matplotlib.pyplot.scatter">
649 <!--<param argument="marker" type="select" label="Marker style" help=""> 671 <!--<param argument="marker" type="select" label="Marker style" help="">
650 <option value="o">o</option> 672 <option value="o">o</option>
651 <option value="v">v</option> 673 <option value="v">v</option>
724 jitter=$method.violin_plot.stripplot.jitter.jitter, 746 jitter=$method.violin_plot.stripplot.jitter.jitter,
725 #if $method.violin_plot.stripplot.jitter.jitter == "True" 747 #if $method.violin_plot.stripplot.jitter.jitter == "True"
726 size=$method.violin_plot.stripplot.jitter.size, 748 size=$method.violin_plot.stripplot.jitter.size,
727 #end if 749 #end if
728 #end if 750 #end if
729 multi_panel=$method.violin_plot.multi_panel.multi_panel, 751 multi_panel=$method.violin_plot.multi_panel.multi_panel,
730 #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) != '' 752 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
731 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) 753 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
732 #end if 754 #end if
733 scale='$method.violin_plot.scale', 755 scale='$method.violin_plot.scale',
734 ]]></token> 756 ]]></token>
761 color='$method.seaborn_violinplot.color', 783 color='$method.seaborn_violinplot.color',
762 palette='$method.seaborn_violinplot.palette', 784 palette='$method.seaborn_violinplot.palette',
763 saturation=$method.seaborn_violinplot.saturation 785 saturation=$method.seaborn_violinplot.saturation
764 ]]></token> 786 ]]></token>
765 <xml name="param_color"> 787 <xml name="param_color">
766 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"/> 788 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
789 <expand macro="sanitize_query" />
790 </param>
767 </xml> 791 </xml>
768 <token name="@CMD_param_color@"><![CDATA[ 792 <token name="@CMD_param_color@"><![CDATA[
769 #if str($method.color) != '' 793 #if str($method.color) != ''
770 #set $color = ([x.strip() for x in str($method.color).split(',')]) 794 #set $color = ([x.strip() for x in str($method.color).split(',')])
771 color=$color, 795 color=$color,
772 #end if 796 #end if
773 ]]></token> 797 ]]></token>
774 <xml name="param_groups"> 798 <xml name="param_groups">
775 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"/> 799 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
800 <expand macro="sanitize_query" />
801 </param>
776 </xml> 802 </xml>
777 <token name="@CMD_params_groups@"><![CDATA[ 803 <token name="@CMD_params_groups@"><![CDATA[
778 #if str($method.groups) != '' 804 #if str($method.groups) != ''
779 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 805 #set $groups=([x.strip() for x in str($method.groups).split(',')])
780 groups=$groups, 806 groups=$groups,
781 #end if 807 #end if
782 ]]></token> 808 ]]></token>
783 <xml name="pl_components"> 809 <xml name="pl_components">
784 <repeat name="components" title="Component"> 810 <repeat name="components" title="Component">
785 <param argument="axis1" type="text" value="1" label="X-Axis" help=""/> 811 <param argument="axis1" type="text" value="1" label="X-Axis" help="">
786 <param argument="axis2" type="text" value="2" label="Y-Axis" help=""/> 812 <expand macro="sanitize_query" />
813 </param>
814 <param argument="axis2" type="text" value="2" label="Y-Axis" help="">
815 <expand macro="sanitize_query" />
816 </param>
787 </repeat> 817 </repeat>
788 </xml> 818 </xml>
789 <token name="@CMD_params_pl_components@"><![CDATA[ 819 <token name="@CMD_params_pl_components@"><![CDATA[
790 #if len($method.plot.components) > 0 820 #if len($method.plot.components) > 0
791 #set $components=[] 821 #set $components=[]
840 <option value="black">black</option> 870 <option value="black">black</option>
841 </param> 871 </param>
842 </xml> 872 </xml>
843 <xml name="param_palette"> 873 <xml name="param_palette">
844 <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 874 <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help="">
845 <option value="">Default</option> 875 <option value="default">Default</option>
846 <expand macro="matplotlib_pyplot_colormap"/> 876 <expand macro="matplotlib_pyplot_colormap"/>
847 </param> 877 </param>
848 </xml> 878 </xml>
849 <xml name="param_color_map"> 879 <xml name="param_color_map">
850 <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> 880 <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
851 <option value="">Default</option> 881 <option value="None">Default</option>
852 <expand macro="matplotlib_pyplot_colormap"/> 882 <expand macro="matplotlib_pyplot_colormap"/>
853 </param> 883 </param>
854 </xml> 884 </xml>
855 <xml name="param_frameon"> 885 <xml name="param_frameon">
856 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/> 886 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
869 size=$method.plot.size, 899 size=$method.plot.size,
870 #end if 900 #end if
871 ]]> 901 ]]>
872 </token> 902 </token>
873 <xml name="param_title"> 903 <xml name="param_title">
874 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> 904 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma">
905 <expand macro="sanitize_query" />
906 </param>
875 </xml> 907 </xml>
876 <token name="@CMD_param_title@"><![CDATA[ 908 <token name="@CMD_param_title@"><![CDATA[
877 #if $method.plot.title 909 #if $method.plot.title
878 title='$method.plot.title', 910 title='$method.plot.title',
879 #end if 911 #end if
948 projection='$method.plot.projection', 980 projection='$method.plot.projection',
949 legend_loc='$method.plot.legend_loc', 981 legend_loc='$method.plot.legend_loc',
950 @CMD_param_legend_fontsize@ 982 @CMD_param_legend_fontsize@
951 legend_fontweight='$method.plot.legend_fontweight', 983 legend_fontweight='$method.plot.legend_fontweight',
952 @CMD_param_size@ 984 @CMD_param_size@
953 #if str($method.plot.color_map) != '' 985 #if str($method.plot.color_map) != 'None'
954 color_map='$method.plot.color_map', 986 color_map='$method.plot.color_map',
955 #end if 987 #end if
956 #if str($method.plot.palette) != '' 988 #if str($method.plot.palette) != ''
957 palette='$method.plot.palette', 989 palette='$method.plot.palette',
958 #end if 990 #end if
976 <param argument="layout" type="select" label="Plotting layout" help=""> 1008 <param argument="layout" type="select" label="Plotting layout" help="">
977 <expand macro="options_layout"/> 1009 <expand macro="options_layout"/>
978 </param> 1010 </param>
979 </xml> 1011 </xml>
980 <xml name="param_root"> 1012 <xml name="param_root">
981 <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."/> 1013 <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.">
1014 <expand macro="sanitize_query" />
1015 </param>
982 </xml> 1016 </xml>
983 <xml name="param_random_state"> 1017 <xml name="param_random_state">
984 <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."/> 1018 <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."/>
985 </xml> 1019 </xml>
986 <xml name="inputs_paga"> 1020 <xml name="inputs_paga">
987 <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."/> 1021 <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."/>
988 <expand macro="param_groups"/> 1022 <expand macro="param_groups"/>
989 <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'."/> 1023 <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'.">
1024 <expand macro="sanitize_query" />
1025 </param>
990 <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=""/> 1026 <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=""/>
991 <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."/> 1027 <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.">
1028 <expand macro="sanitize_query" />
1029 </param>
992 <expand macro="param_layout"/> 1030 <expand macro="param_layout"/>
993 <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=""/> 1031 <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=""/>
994 <expand macro="param_random_state"/> 1032 <expand macro="param_random_state"/>
995 <expand macro="param_root"/> 1033 <expand macro="param_root"/>
996 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'"/> 1034 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'">
997 <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"/> 1035 <expand macro="sanitize_query" />
998 <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."/> 1036 </param>
1037 <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">
1038 <expand macro="sanitize_query" />
1039 </param>
1040 <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.">
1041 <expand macro="sanitize_query" />
1042 </param>
999 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> 1043 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
1000 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/> 1044 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
1001 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/> 1045 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
1002 <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=""/> 1046 <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=""/>
1003 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/> 1047 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>
1064 </token> 1108 </token>
1065 <xml name="param_swap_axes"> 1109 <xml name="param_swap_axes">
1066 <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'."/> 1110 <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'."/>
1067 </xml> 1111 </xml>
1068 <xml name="gene_symbols"> 1112 <xml name="gene_symbols">
1069 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"/> 1113 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
1114 <expand macro="sanitize_query" />
1115 </param>
1070 </xml> 1116 </xml>
1071 <xml name="param_n_genes"> 1117 <xml name="param_n_genes">
1072 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> 1118 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
1073 </xml> 1119 </xml>
1074 <xml name="pl_dotplot"> 1120 <xml name="pl_dotplot">
1089 #end if 1135 #end if
1090 @CMD_params_matplotlib_pyplot_scatter@ 1136 @CMD_params_matplotlib_pyplot_scatter@
1091 ]]> 1137 ]]>
1092 </token> 1138 </token>
1093 <xml name="param_key"> 1139 <xml name="param_key">
1094 <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'"/> 1140 <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'">
1141 <expand macro="sanitize_query" />
1142 </param>
1095 </xml> 1143 </xml>
1096 <xml name="pl_heatmap"> 1144 <xml name="pl_heatmap">
1097 <expand macro="param_swap_axes"/> 1145 <expand macro="param_swap_axes"/>
1098 <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."/> 1146 <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."/>
1099 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow"> 1147 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">