Mercurial > repos > iuc > scanpy_normalize
comparison macros.xml @ 7:a407e7f8bdc1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author | iuc |
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date | Wed, 20 May 2020 16:09:36 -0400 |
parents | 3bcd5445cd7a |
children | 5342ce58cd1e |
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6:3bcd5445cd7a | 7:a407e7f8bdc1 |
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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="'" /> | |
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"> |