Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison macros.xml @ 3:ac8e59e87ce3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d"
author iuc
date Thu, 12 Dec 2019 09:25:42 -0500
parents dc2de14881ba
children 766be978777a
comparison
equal deleted inserted replaced
2:dc2de14881ba 3:ac8e59e87ce3
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@+galaxy0]]></token> 4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy1]]></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>
349 <option value="jet">jet (Miscellaneous)</option> 349 <option value="jet">jet (Miscellaneous)</option>
350 <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option> 350 <option value="nipy_spectral">nipy_spectral (Miscellaneous)</option>
351 <option value="gist_ncar">gist_ncar (Miscellaneous)</option> 351 <option value="gist_ncar">gist_ncar (Miscellaneous)</option>
352 </xml> 352 </xml>
353 <xml name="param_groupby"> 353 <xml name="param_groupby">
354 <param argument="groupby" type="text" value="" optional="true" label="The key of the observation grouping to consider" help="If it is given, the heatmap 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`."/> 354 <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'."/>
355 </xml> 355 </xml>
356 <xml name="param_use_raw"> 356 <xml name="param_use_raw">
357 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/> 357 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use 'raw' attribute of input if present" help=""/>
358 </xml> 358 </xml>
359 <xml name="param_log"> 359 <xml name="param_log">
360 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/> 360 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>
361 </xml> 361 </xml>
362 <xml name="pl_figsize"> 362 <xml name="pl_figsize">
376 376
377 ]]></token> 377 ]]></token>
378 <xml name="pl_var_names"> 378 <xml name="pl_var_names">
379 <conditional name="var_names"> 379 <conditional name="var_names">
380 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > 380 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
381 <option value="all">All variables in `adata.var_names`</option> 381 <option value="all">All variables in 'adata.var_names'</option>
382 <option value="custom">Subset of variables in `adata.var_names`</option> 382 <option value="custom">Subset of variables in 'adata.var_names'</option>
383 </param> 383 </param>
384 <when value="all"/> 384 <when value="all"/>
385 <when value="custom"> 385 <when value="custom">
386 <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"/> 386 <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"/>
387 </when> 387 </when>
388 </conditional> 388 </conditional>
389 </xml> 389 </xml>
390 <xml name="param_num_categories"> 390 <xml name="param_num_categories">
391 <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."/> 391 <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."/>
402 </xml> 402 </xml>
403 <xml name="param_var_group_rotation"> 403 <xml name="param_var_group_rotation">
404 <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"/> 404 <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"/>
405 </xml> 405 </xml>
406 <xml name="param_layer"> 406 <xml name="param_layer">
407 <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`."/> 407 <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'."/>
408 </xml> 408 </xml>
409 <token name="@CMD_param_plot_inputs@"><![CDATA[ 409 <token name="@CMD_param_plot_inputs@"><![CDATA[
410 adata, 410 adata,
411 save='.$format', 411 save='.$format',
412 show=False, 412 show=False,
413 ]]></token> 413 ]]></token>
414 <xml name="params_plots"> 414 <xml name="params_inputs">
415 <expand macro="pl_var_names"/> 415 <expand macro="pl_var_names"/>
416 <expand macro="param_groupby"/> 416 <expand macro="param_groupby"/>
417 <expand macro="param_num_categories"/>
418 </xml>
419 <token name="@CMD_params_inputs@"><![CDATA[
420 #if $method.var_names.type == 'all'
421 var_names=adata.var_names,
422 #else
423 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
424 var_names=$var_names,
425 #end if
426 #if str($method.groupby) != ''
427 groupby='$method.groupby',
428 #end if
429 num_categories=$method.num_categories,
430 ]]></token>
431 <xml name="params_plots">
417 <expand macro="param_log"/> 432 <expand macro="param_log"/>
418 <expand macro="param_use_raw"/> 433 <expand macro="param_use_raw"/>
419 <expand macro="param_num_categories"/>
420 <expand macro="param_dendrogram"/> 434 <expand macro="param_dendrogram"/>
421 <expand macro="pl_var_group_positions"/> 435 <expand macro="pl_var_group_positions"/>
422 <expand macro="param_var_group_rotation"/> 436 <expand macro="param_var_group_rotation"/>
423 <expand macro="pl_figsize"/> 437 <expand macro="pl_figsize"/>
424 <expand macro="param_layer"/> 438 <expand macro="param_layer"/>
425 </xml> 439 </xml>
426 <token name="@CMD_params_plots@"><![CDATA[ 440 <token name="@CMD_params_plots@"><![CDATA[
427 #if $method.var_names.type == 'all'
428 var_names=adata.var_names,
429 #else
430 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
431 var_names=$var_names,
432 #end if
433 #if str($method.groupby) != ''
434 groupby='$method.groupby',
435 #end if
436 log=$method.log, 441 log=$method.log,
437 use_raw=$method.use_raw, 442 use_raw=$method.use_raw,
438 num_categories=$method.num_categories,
439 dendrogram=$method.dendrogram, 443 dendrogram=$method.dendrogram,
440 #if len($method.var_group_positions) > 0: 444 #if len($method.var_group_positions) > 0:
441 #set $var_group_positions=[] 445 #set $var_group_positions=[]
442 #set $var_group_labels=[] 446 #set $var_group_labels=[]
443 #for $i, $s in enumerate($method.var_group_positions) 447 #for $i, $s in enumerate($method.var_group_positions)
671 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help=""> 675 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
672 <option value="True">Yes</option> 676 <option value="True">Yes</option>
673 <option value="False">No</option> 677 <option value="False">No</option>
674 </param> 678 </param>
675 <when value="True"> 679 <when value="True">
676 <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/> 680 <param argument="size" type="float" min="0" value="1" label="Size of the jitter points" help=""/>
677 </when> 681 </when>
678 <when value="False"/> 682 <when value="False"/>
679 </conditional> 683 </conditional>
680 </when> 684 </when>
681 <when value="False"/> 685 <when value="False"/>
740 color='$method.seaborn_violinplot.color', 744 color='$method.seaborn_violinplot.color',
741 palette='$method.seaborn_violinplot.palette', 745 palette='$method.seaborn_violinplot.palette',
742 saturation=$method.seaborn_violinplot.saturation, 746 saturation=$method.seaborn_violinplot.saturation,
743 ]]></token> 747 ]]></token>
744 <xml name="param_color"> 748 <xml name="param_color">
745 <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`"/> 749 <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'"/>
746 </xml> 750 </xml>
747 <token name="@CMD_param_color@"><![CDATA[ 751 <token name="@CMD_param_color@"><![CDATA[
748 #if str($method.color) != '' 752 #if str($method.color) != ''
749 #set $color = ([x.strip() for x in str($method.color).split(',')]) 753 #set $color = ([x.strip() for x in str($method.color).split(',')])
750 color=$color, 754 color=$color,
751 #end if 755 #end if
752 ]]></token> 756 ]]></token>
753 <xml name="pl_groups"> 757 <xml name="param_groups">
754 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/> 758 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"/>
755 </xml> 759 </xml>
756 <token name="@CMD_params_pl_groups@"><![CDATA[ 760 <token name="@CMD_params_groups@"><![CDATA[
757 #if str($method.groups) != '' 761 #if str($method.groups) != ''
758 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 762 #set $groups=([x.strip() for x in str($method.groups).split(',')])
759 groups=$groups, 763 groups=$groups,
760 #end if 764 #end if
761 ]]></token> 765 ]]></token>
762 <xml name="pl_components"> 766 <xml name="pl_components">
763 <repeat name="components" title="Component"> 767 <repeat name="components" title="Component">
764 <param argument="axis1" type="text" value="1" label="Axis 1" help=""/> 768 <param argument="axis1" type="text" value="1" label="X-Axis" help=""/>
765 <param argument="axis2" type="text" value="2" label="Axis 2" help=""/> 769 <param argument="axis2" type="text" value="2" label="Y-Axis" help=""/>
766 </repeat> 770 </repeat>
767 </xml> 771 </xml>
768 <token name="@CMD_params_pl_components@"><![CDATA[ 772 <token name="@CMD_params_pl_components@"><![CDATA[
769 #if len($method.plot.components) > 0 773 #if len($method.plot.components) > 0
770 #set $components=[] 774 #set $components=[]
800 </param> 804 </param>
801 </xml> 805 </xml>
802 <xml name="param_legend_fontsize"> 806 <xml name="param_legend_fontsize">
803 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/> 807 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/>
804 </xml> 808 </xml>
809 <token name="@CMD_param_legend_fontsize@"><![CDATA[
810 #if str($method.plot.legend_fontsize) != ''
811 legend_fontsize=$method.plot.legend_fontsize,
812 #end if
813 ]]>
814 </token>
805 <xml name="param_legend_fontweight"> 815 <xml name="param_legend_fontweight">
806 <param argument="legend_fontweight" type="select" label="Legend font weight" help=""> 816 <param argument="legend_fontweight" type="select" label="Legend font weight" help="">
807 <option value="light">light</option> 817 <option value="light">light</option>
808 <option value="normal" selected="true">normal</option> 818 <option value="normal" selected="true">normal</option>
809 <option value="medium">medium</option> 819 <option value="medium">medium</option>
812 <option value="heavy">heavy</option> 822 <option value="heavy">heavy</option>
813 <option value="black">black</option> 823 <option value="black">black</option>
814 </param> 824 </param>
815 </xml> 825 </xml>
816 <xml name="param_palette"> 826 <xml name="param_palette">
817 <param argument="palette" type="select" label="Colors to use for plotting g categorical annotation groups" help=""> 827 <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help="">
828 <option value="">Default</option>
818 <expand macro="matplotlib_pyplot_colormap"/> 829 <expand macro="matplotlib_pyplot_colormap"/>
819 </param> 830 </param>
820 </xml> 831 </xml>
821 <xml name="param_color_map"> 832 <xml name="param_color_map">
822 <param argument="color_map" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 833 <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
834 <option value="">Default</option>
823 <expand macro="matplotlib_pyplot_colormap"/> 835 <expand macro="matplotlib_pyplot_colormap"/>
824 </param> 836 </param>
825 </xml> 837 </xml>
826 <xml name="param_frameon"> 838 <xml name="param_frameon">
827 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/> 839 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
833 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/> 845 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/>
834 </xml> 846 </xml>
835 <xml name="param_size"> 847 <xml name="param_size">
836 <param argument="size" type="float" optional="true" value="" label="Point size" help=""/> 848 <param argument="size" type="float" optional="true" value="" label="Point size" help=""/>
837 </xml> 849 </xml>
850 <token name="@CMD_param_size@"><![CDATA[
851 #if str($method.plot.size) != ''
852 size=$method.plot.size,
853 #end if
854 ]]>
855 </token>
838 <xml name="param_title"> 856 <xml name="param_title">
839 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> 857 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/>
840 </xml> 858 </xml>
859 <token name="@CMD_param_title@"><![CDATA[
860 #if $method.plot.title
861 title='$method.plot.title',
862 #end if
863 ]]>
864 </token>
841 <xml name="param_sort_order"> 865 <xml name="param_sort_order">
842 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/> 866 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
843 </xml> 867 </xml>
844 <xml name="param_sort_order"> 868 <xml name="param_sort_order">
845 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/> 869 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Sort order?" help="For continuous annotations used as color parameter, plot data points with higher values on top of others."/>
877 edges=False, 901 edges=False,
878 #end if 902 #end if
879 ]]> 903 ]]>
880 </token> 904 </token>
881 <xml name="param_arrows"> 905 <xml name="param_arrows">
882 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/> 906 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
883 </xml> 907 </xml>
884 <xml name="param_cmap"> 908 <xml name="param_cmap">
885 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 909 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
886 <expand macro="matplotlib_pyplot_colormap"/> 910 <expand macro="matplotlib_pyplot_colormap"/>
887 </param> 911 </param>
892 <expand macro="param_projection"/> 916 <expand macro="param_projection"/>
893 <expand macro="param_legend_loc"/> 917 <expand macro="param_legend_loc"/>
894 <expand macro="param_legend_fontsize"/> 918 <expand macro="param_legend_fontsize"/>
895 <expand macro="param_legend_fontweight"/> 919 <expand macro="param_legend_fontweight"/>
896 <expand macro="param_size"/> 920 <expand macro="param_size"/>
921 <expand macro="param_color_map"/>
897 <expand macro="param_palette"/> 922 <expand macro="param_palette"/>
898 <expand macro="param_frameon"/> 923 <expand macro="param_frameon"/>
899 <expand macro="param_ncols"/> 924 <expand macro="param_ncols"/>
900 <expand macro="param_wspace"/> 925 <expand macro="param_wspace"/>
901 <expand macro="param_hspace"/> 926 <expand macro="param_hspace"/>
903 </section> 928 </section>
904 </xml> 929 </xml>
905 <token name="@CMD_pl_attribute_section@"><![CDATA[ 930 <token name="@CMD_pl_attribute_section@"><![CDATA[
906 projection='$method.plot.projection', 931 projection='$method.plot.projection',
907 legend_loc='$method.plot.legend_loc', 932 legend_loc='$method.plot.legend_loc',
908 #if str($method.plot.legend_fontsize) != '' 933 @CMD_param_legend_fontsize@
909 legend_fontsize=$method.plot.legend_fontsize,
910 #end if
911 legend_fontweight='$method.plot.legend_fontweight', 934 legend_fontweight='$method.plot.legend_fontweight',
912 #if str($method.plot.size) != '' 935 @CMD_param_size@
913 size=$method.plot.size, 936 #if str($method.plot.color_map) != ''
914 #end if 937 color_map='$method.plot.color_map',
938 #end if
939 #if str($method.plot.palette) != ''
915 palette='$method.plot.palette', 940 palette='$method.plot.palette',
941 #end if
916 frameon=$method.plot.frameon, 942 frameon=$method.plot.frameon,
917 ncols=$method.plot.ncols, 943 ncols=$method.plot.ncols,
918 wspace=$method.plot.wspace, 944 wspace=$method.plot.wspace,
919 hspace=$method.plot.hspace, 945 hspace=$method.plot.hspace,
920 #if $method.plot.title 946 @CMD_param_title@
921 title='$method.plot.title',
922 #end if
923 ]]> 947 ]]>
924 </token> 948 </token>
925 <xml name="options_layout"> 949 <xml name="options_layout">
926 <option value="fa">fa: ForceAtlas2</option> 950 <option value="fa">fa: ForceAtlas2</option>
927 <option value="fr">fr: Fruchterman-Reingold</option> 951 <option value="fr">fr: Fruchterman-Reingold</option>
935 <param argument="layout" type="select" label="Plotting layout" help=""> 959 <param argument="layout" type="select" label="Plotting layout" help="">
936 <expand macro="options_layout"/> 960 <expand macro="options_layout"/>
937 </param> 961 </param>
938 </xml> 962 </xml>
939 <xml name="param_root"> 963 <xml name="param_root">
940 <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."/> 964 <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."/>
941 </xml> 965 </xml>
942 <xml name="param_random_state"> 966 <xml name="param_random_state">
943 <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."/> 967 <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."/>
944 </xml> 968 </xml>
945 <xml name="inputs_paga"> 969 <xml name="inputs_paga">
946 <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."/> 970 <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."/>
947 <expand macro="pl_groups"/> 971 <expand macro="param_groups"/>
948 <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'."/> 972 <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'."/>
949 <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=""/> 973 <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=""/>
950 <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."/> 974 <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."/>
951 <expand macro="param_layout"/> 975 <expand macro="param_layout"/>
952 <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=""/> 976 <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=""/>
953 <expand macro="param_random_state"/> 977 <expand macro="param_random_state"/>
954 <expand macro="param_root"/> 978 <expand macro="param_root"/>
955 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/> 979 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for '.uns['paga']', e.g. 'transistions_confidence'"/>
956 <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"/> 980 <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"/>
957 <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."/> 981 <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."/>
958 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> 982 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
959 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/> 983 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
960 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/> 984 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
1020 #end if 1044 #end if
1021 frameon=$method.frameon, 1045 frameon=$method.frameon,
1022 ]]> 1046 ]]>
1023 </token> 1047 </token>
1024 <xml name="param_swap_axes"> 1048 <xml name="param_swap_axes">
1025 <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`."/> 1049 <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'."/>
1026 </xml> 1050 </xml>
1027 <xml name="gene_symbols"> 1051 <xml name="gene_symbols">
1028 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in `.var` that stores gene symbols"/> 1052 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"/>
1029 </xml> 1053 </xml>
1030 <xml name="n_genes"> 1054 <xml name="param_n_genes">
1031 <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/> 1055 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
1032 </xml> 1056 </xml>
1057 <xml name="pl_dotplot">
1058 <param argument="color_map" type="select" label="Color palette">
1059 <expand macro="matplotlib_pyplot_colormap"/>
1060 </param>
1061 <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
1062 <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
1063 <expand macro="section_matplotlib_pyplot_scatter"/>
1064 </xml>
1065 <token name="@CMD_pl_dotplot@"><![CDATA[
1066 color_map='$method.color_map',
1067 #if str($method.dot_max) != ''
1068 dot_max=$method.dot_max,
1069 #end if
1070 #if str($method.dot_min) != ''
1071 dot_min=$method.dot_min,
1072 #end if
1073 @CMD_params_matplotlib_pyplot_scatter@
1074 ]]>
1075 </token>
1076 <xml name="param_key">
1077 <param argument="key" type="text" value="" label="Key used to store the ranking results in 'uns'"/>
1078 </xml>
1079 <xml name="pl_heatmap">
1080 <expand macro="param_swap_axes"/>
1081 <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."/>
1082 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
1083 <expand macro="param_cmap"/>
1084 <param name="interpolation" type="select" label="Interpolation method" help="">
1085 <option value="None">none</option>
1086 <option value="nearest">nearest</option>
1087 <option value="bilinear">bilinear</option>
1088 <option value="bicubic">bicubic</option>
1089 <option value="spline16">spline16</option>
1090 <option value="spline36">spline36</option>
1091 <option value="hanning">hanning</option>
1092 <option value="hamming">hamming</option>
1093 <option value="hermite">hermite</option>
1094 <option value="kaiser">kaiser</option>
1095 <option value="quadric">quadric</option>
1096 <option value="catrom">catrom</option>
1097 <option value="gaussian">gaussian</option>
1098 <option value="bessel">bessel</option>
1099 <option value="sinc">sinc</option>
1100 <option value="mitchell">mitchell</option>
1101 <option value="lanczos">lanczos</option>
1102 </param>
1103 <expand macro="param_alpha"/>
1104 <expand macro="param_vmin"/>
1105 <expand macro="param_vmax"/>
1106 <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">
1107 <option value="upper">Upper</option>
1108 <option value="lower">Lower</option>
1109 </param>
1110 </section>
1111 </xml>
1112 <token name="@CMD_pl_heatmap@"><![CDATA[
1113 swap_axes=$method.swap_axes,
1114 show_gene_labels=$method.show_gene_labels,
1115 cmap='$method.matplotlib_pyplot_imshow.cmap',
1116 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
1117 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
1118 #end if
1119 #if $method.matplotlib_pyplot_imshow.alpha
1120 alpha=$method.matplotlib_pyplot_imshow.alpha,
1121 #end if
1122 #if $method.matplotlib_pyplot_imshow.vmin
1123 vmin=$method.matplotlib_pyplot_imshow.vmin,
1124 #end if
1125 #if $method.matplotlib_pyplot_imshow.vmax
1126 vmax=$method.matplotlib_pyplot_imshow.vmax,
1127 #end if
1128 origin='$method.matplotlib_pyplot_imshow.origin'
1129 ]]>
1130 </token>
1131 <xml name="pl_rank_genes_groups_ext">
1132 <expand macro="param_groups"/>
1133 <expand macro="param_n_genes"/>
1134 <expand macro="param_key"/>
1135 </xml>
1136 <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
1137 @CMD_params_groups@
1138 #if str($method.n_genes) != ''
1139 n_genes=$method.n_genes,
1140 #end if
1141 #if str($method.key) != ''
1142 key='$method.key',
1143 #end if
1144 ]]>
1145 </token>
1146 <xml name="pl_matrixplot">
1147 <expand macro="param_swap_axes"/>
1148 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
1149 <param argument="cmap" type="select" label="Color palette">
1150 <expand macro="seaborn_color_palette_options"/>
1151 </param>
1152 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
1153 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
1154 <expand macro="param_matplotlib_pyplot_edgecolors"/>
1155 <expand macro="param_alpha"/>
1156 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
1157 </section>
1158 </xml>
1159 <token name="@CMD_pl_matrixplot@"><![CDATA[
1160 swap_axes=$method.swap_axes,
1161 cmap='$method.matplotlib_pyplot_pcolor.cmap',
1162 #if $method.matplotlib_pyplot_pcolor.vmin
1163 vmin=$method.matplotlib_pyplot_pcolor.vmin,
1164 #end if
1165 #if $method.matplotlib_pyplot_pcolor.vmax
1166 vmax=$method.matplotlib_pyplot_pcolor.vmax,
1167 #end if
1168 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
1169 #if $method.matplotlib_pyplot_pcolor.alpha
1170 alpha=$method.matplotlib_pyplot_pcolor.alpha,
1171 #end if
1172 snap=$method.matplotlib_pyplot_pcolor.snap
1173 ]]>
1174 </token>
1175 <xml name="pl_stacked_violin">
1176 <expand macro="param_swap_axes"/>
1177 <section name="violin_plot" title="Violin plot attributes">
1178 <expand macro="conditional_stripplot"/>
1179 <expand macro="param_scale"/>
1180 </section>
1181 <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
1182 <option value="muted">muted</option>
1183 <expand macro="seaborn_color_palette_options"/>
1184 </param>
1185 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
1186 <option value="None">No standardization</option>
1187 <option value="var">Standardization on variable</option>
1188 <option value="obs">Standardization on observation</option>
1189 </param>
1190 <expand macro="seaborn_violinplot"/>
1191 </xml>
1192 <token name="@CMD_pl_stacked_violin@"><![CDATA[
1193 swap_axes=$method.swap_axes,
1194 @CMD_conditional_stripplot@
1195 scale='$method.violin_plot.scale',
1196 row_palette='$method.row_palette',
1197 #if str($method.standard_scale) != 'None'
1198 standard_scale='$method.standard_scale',
1199 #end if
1200 @CMD_params_seaborn_violinplot@
1201 ]]>
1202 </token>
1033 </macros> 1203 </macros>