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comparison macros.xml @ 1:072b759d0fca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:21:53 -0400
parents 729198e3330c
children 791469a96577
comparison
equal deleted inserted replaced
0:729198e3330c 1:072b759d0fca
1 <macros> 1 <macros>
2 <token name="@version@">1.4</token> 2 <token name="@version@">1.4.4</token>
3 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> 3 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@version@">scanpy</requirement> 6 <requirement type="package" version="@version@">scanpy</requirement>
7 <requirement type="package" version="2.0.17">loompy</requirement> 7 <requirement type="package" version="2.0.17">loompy</requirement>
8 <requirement type="package" version="2.9.0">h5py</requirement>
9 <requirement type="package" version="0.7.0">leidenalg</requirement>
8 <yield /> 10 <yield />
9 </requirements> 11 </requirements>
10 </xml> 12 </xml>
11 <xml name="citations"> 13 <xml name="citations">
12 <citations> 14 <citations>
13 <citation type="doi">10.1186/s13059-017-1382-0</citation> 15 <citation type="doi">10.1186/s13059-017-1382-0</citation>
14 </citations> 16 </citations>
15 </xml> 17 </xml>
16 <xml name="version_command"> 18 <xml name="version_command">
17 <version_command><![CDATA[python -c "import scanpy.api as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> 19 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
18 </xml> 20 </xml>
19 <token name="@CMD@"><![CDATA[ 21 <token name="@CMD@"><![CDATA[
22 cp '$adata' 'anndata.h5ad' &&
20 cat '$script_file' && 23 cat '$script_file' &&
21 python '$script_file' 24 python '$script_file' &&
25 ls .
22 ]]> 26 ]]>
23 </token> 27 </token>
24 <token name="@CMD_imports@"><![CDATA[ 28 <token name="@CMD_imports@"><![CDATA[
25 import scanpy.api as sc 29 import scanpy as sc
26 import pandas as pd 30 import pandas as pd
27 import numpy as np 31 import numpy as np
28 ]]> 32 ]]>
29 </token> 33 </token>
30 <xml name="inputs_anndata"> 34 <xml name="inputs_anndata">
31 <conditional name="input"> 35 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
32 <param name="format" type="select" label="Format for the annotated data matrix">
33 <option value="loom">loom</option>
34 <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
35 </param>
36 <when value="loom">
37 <param name="adata" type="data" format="loom" label="Annotated data matrix"/>
38 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
39 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
40 <param name="x_name" type="text" value="spliced" label="X_name"/>
41 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
42 <param name="var_names" type="text" value="Gene" label="var_names"/>
43 </when>
44 <when value="h5ad">
45 <param name="adata" type="data" format="h5" label="Annotated data matrix"/>
46 </when>
47 </conditional>
48 </xml> 36 </xml>
49 <token name="@CMD_read_inputs@"><![CDATA[ 37 <token name="@CMD_read_inputs@"><![CDATA[
50 #if $input.format == 'loom' 38 adata = sc.read('anndata.h5ad')
51 adata = sc.read_loom(
52 '$input.adata',
53 sparse=$input.sparse,
54 cleanup=$input.cleanup,
55 X_name='$input.x_name',
56 obs_names='$input.obs_names',
57 var_names='$input.var_names')
58 #else if $input.format == 'h5ad'
59 adata = sc.read_h5ad('$input.adata')
60 #end if
61 ]]> 39 ]]>
62 </token> 40 </token>
63 <xml name="anndata_output_format">
64 <param name="anndata_output_format" type="select" label="Format to write the annotated data matrix">
65 <option value="loom">loom</option>
66 <option value="h5ad">h5ad-formatted hdf5 (anndata)</option>
67 </param>
68 </xml>
69 <xml name="anndata_modify_output_input">
70 <conditional name="modify_anndata">
71 <param name="modify_anndata" type="select" label="Return modify annotate data matrix?">
72 <option value="true">Yes</option>
73 <option value="false">No</option>
74 </param>
75 <when value="true">
76 <expand macro="anndata_output_format"/>
77 </when>
78 <when value="false"/>
79 </conditional>
80 </xml>
81 <xml name="anndata_outputs"> 41 <xml name="anndata_outputs">
82 <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"> 42 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
83 <filter>anndata_output_format == 'h5ad'</filter>
84 </data>
85 <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
86 <filter>anndata_output_format == 'loom'</filter>
87 </data>
88 </xml>
89 <xml name="anndata_modify_outputs">
90 <data name="anndata_out_h5ad" format="h5" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix">
91 <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'h5ad'</filter>
92 </data>
93 <data name="anndata_out_loom" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
94 <filter>modify_anndata['modify_anndata'] == 'true' and modify_anndata['anndata_output_format'] == 'loom'</filter>
95 </data>
96 </xml> 43 </xml>
97 <token name="@CMD_anndata_write_outputs@"><![CDATA[ 44 <token name="@CMD_anndata_write_outputs@"><![CDATA[
98 #if $anndata_output_format == 'loom'
99 adata.write_loom('anndata.loom')
100 #else if $anndata_output_format == 'h5ad'
101 adata.write('anndata.h5ad') 45 adata.write('anndata.h5ad')
102 #end if
103 ]]>
104 </token>
105 <token name="@CMD_anndata_write_modify_outputs@"><![CDATA[
106 #if $modify_anndata.modify_anndata == 'true'
107 #if $modify_anndata.anndata_output_format == 'loom'
108 adata.write_loom('anndata.loom')
109 #elif $modify_anndata.anndata_output_format == 'h5ad'
110 adata.write('anndata.h5ad')
111 #end if
112 #end if
113 ]]> 46 ]]>
114 </token> 47 </token>
115 <xml name="svd_solver"> 48 <xml name="svd_solver">
116 <param name="svd_solver" type="select" label="SVD solver to use" help=""> 49 <param name="svd_solver" type="select" label="SVD solver to use" help="">
117 <option value="auto">Automatically chosen depending on the size of the problem</option> 50 <option value="auto">Automatically chosen depending on the size of the problem</option>
421 </xml> 354 </xml>
422 <xml name="param_use_raw"> 355 <xml name="param_use_raw">
423 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/> 356 <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use `raw` attribute of input if present" help=""/>
424 </xml> 357 </xml>
425 <xml name="param_log"> 358 <xml name="param_log">
426 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?" help=""/> 359 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Use the log of the values?"/>
427 </xml> 360 </xml>
428 <xml name="pl_figsize"> 361 <xml name="pl_figsize">
429 <conditional name="figsize"> 362 <conditional name="figsize">
430 <param name="test" type="select" label="Custom figure size" > 363 <param name="test" type="select" label="Custom figure size" >
431 <option value="yes">Yes</option> 364 <option value="yes">Yes</option>
471 </xml> 404 </xml>
472 <xml name="param_layer"> 405 <xml name="param_layer">
473 <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`."/> 406 <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`."/>
474 </xml> 407 </xml>
475 <token name="@CMD_param_plot_inputs@"><![CDATA[ 408 <token name="@CMD_param_plot_inputs@"><![CDATA[
476 adata=adata, 409 adata,
477 save='.$format', 410 save='.$format',
478 show=False, 411 show=False,
479 ]]></token> 412 ]]></token>
480 <xml name="params_plots"> 413 <xml name="params_plots">
481 <expand macro="pl_var_names"/> 414 <expand macro="pl_var_names"/>
510 #silent $var_group_positions.append((int($s.start), int($s.end))) 443 #silent $var_group_positions.append((int($s.start), int($s.end)))
511 #silent $var_group_labels.append(str($s.label)) 444 #silent $var_group_labels.append(str($s.label))
512 #end for 445 #end for
513 var_group_positions=$var_group_positions, 446 var_group_positions=$var_group_positions,
514 var_group_labels=$var_group_labels, 447 var_group_labels=$var_group_labels,
515 #else
516 var_group_positions=None,
517 var_group_labels=None,
518 #end if 448 #end if
519 #if $method.var_group_rotation 449 #if $method.var_group_rotation
520 var_group_rotation=$method.var_group_rotation, 450 var_group_rotation=$method.var_group_rotation,
521 #end if 451 #end if
522 #if $method.figsize.test == 'yes' 452 #if $method.figsize.test == 'yes'
727 alpha=$method.matplotlib_pyplot_scatter.alpha, 657 alpha=$method.matplotlib_pyplot_scatter.alpha,
728 #end if 658 #end if
729 linewidths=$method.matplotlib_pyplot_scatter.linewidths, 659 linewidths=$method.matplotlib_pyplot_scatter.linewidths,
730 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' 660 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
731 ]]></token> 661 ]]></token>
732 <xml name="section_violin_plots"> 662 <xml name="conditional_stripplot">
733 <section name="violin_plot" title="Violin plot attributes"> 663 <conditional name="stripplot">
734 <conditional name="stripplot"> 664 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
735 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help=""> 665 <option value="True">Yes</option>
736 <option value="True">Yes</option> 666 <option value="False">No</option>
737 <option value="False">No</option>
738 </param>
739 <when value="True">
740 <conditional name="jitter">
741 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
742 <option value="True">Yes</option>
743 <option value="False">No</option>
744 </param>
745 <when value="True">
746 <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/>
747 </when>
748 <when value="False"/>
749 </conditional>
750 </when>
751 <when value="False"/>
752 </conditional>
753 <conditional name="multi_panel">
754 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when `groupby is not provided">
755 <option value="True">Yes</option>
756 <option value="False" selected="true">No</option>
757 </param>
758 <when value="True">
759 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
760 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
761 </when>
762 <when value="False"/>
763 </conditional>
764 <param argument="scale" type="select" label="Method used to scale the width of each violin">
765 <option value="area">area: each violin will have the same area</option>
766 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
767 <option value="width" selected="true">width: each violin will have the same width</option>
768 </param> 667 </param>
769 </section> 668 <when value="True">
669 <conditional name="jitter">
670 <param argument="jitter" type="select" label="Add a jitter to the stripplot" help="">
671 <option value="True">Yes</option>
672 <option value="False">No</option>
673 </param>
674 <when value="True">
675 <param argument="size" type="integer" min="0" value="1" label="Size of the jitter points" help=""/>
676 </when>
677 <when value="False"/>
678 </conditional>
679 </when>
680 <when value="False"/>
681 </conditional>
682 </xml>
683 <token name="@CMD_conditional_stripplot@"><![CDATA[
684 stripplot=$method.violin_plot.stripplot.stripplot,
685 #if $method.violin_plot.stripplot.stripplot == "True"
686 jitter=$method.violin_plot.stripplot.jitter.jitter,
687 #if $method.violin_plot.stripplot.jitter.jitter == "True"
688 size=$method.violin_plot.stripplot.jitter.size,
689 #end if
690 #end if
691 ]]></token>
692 <xml name="param_scale">
693 <param argument="scale" type="select" label="Method used to scale the width of each violin">
694 <option value="area">area: each violin will have the same area</option>
695 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
696 <option value="width" selected="true">width: each violin will have the same width</option>
697 </param>
770 </xml> 698 </xml>
771 <token name="@CMD_params_violin_plots@"><![CDATA[ 699 <token name="@CMD_params_violin_plots@"><![CDATA[
772 stripplot=$method.violin_plot.stripplot.stripplot, 700 stripplot=$method.violin_plot.stripplot.stripplot,
773 #if $method.violin_plot.stripplot.stripplot == "True" 701 #if $method.violin_plot.stripplot.stripplot == "True"
774 jitter=$method.violin_plot.stripplot.jitter.jitter, 702 jitter=$method.violin_plot.stripplot.jitter.jitter,
775 #if $method.violin_plot.stripplot.jitter.jitter == "True" 703 #if $method.violin_plot.stripplot.jitter.jitter == "True"
776 size=$method.violin_plot.stripplot.jitter.size, 704 size=$method.violin_plot.stripplot.jitter.size,
777 #end if 705 #end if
778 #end if 706 #end if
779 multi_panel=$method.violin_plot.multi_panel.multi_panel, 707 multi_panel=$method.violin_plot.multi_panel.multi_panel,
780 #if $method.multi_panel.violin_plot.multi_panel == "True" and $method.violin_plot.multi_panel.width and $method.violin_plot.multi_panel.height 708 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
781 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) 709 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
782 #end if 710 #end if
783 scale='$method.violin_plot.scale', 711 scale='$method.violin_plot.scale',
784 ]]></token> 712 ]]></token>
785 <xml name="seaborn_violinplot"> 713 <xml name="seaborn_violinplot">
811 color='$method.seaborn_violinplot.color', 739 color='$method.seaborn_violinplot.color',
812 palette='$method.seaborn_violinplot.palette', 740 palette='$method.seaborn_violinplot.palette',
813 saturation=$method.seaborn_violinplot.saturation, 741 saturation=$method.seaborn_violinplot.saturation,
814 ]]></token> 742 ]]></token>
815 <xml name="param_color"> 743 <xml name="param_color">
816 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes`" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/> 744 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either `.obs` or `.var`"/>
817 </xml> 745 </xml>
818 <token name="@CMD_param_color@"><![CDATA[ 746 <token name="@CMD_param_color@"><![CDATA[
819 #if str($method.color) != '' 747 #if str($method.color) != ''
820 #set $color = ([x.strip() for x in str($method.color).split(',')]) 748 #set $color = ([x.strip() for x in str($method.color).split(',')])
821 color=$color, 749 color=$color,
822 #else
823 color=None,
824 #end if 750 #end if
825 ]]></token> 751 ]]></token>
826 <xml name="pl_groups"> 752 <xml name="pl_groups">
827 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/> 753 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations, comma-separated" help=""/>
828 </xml> 754 </xml>
829 <token name="@CMD_params_pl_groups@"><![CDATA[ 755 <token name="@CMD_params_pl_groups@"><![CDATA[
830 #if str($method.groups) != '' 756 #if str($method.groups) != ''
831 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 757 #set $groups=([x.strip() for x in str($method.groups).split(',')])
832 groups=$groups, 758 groups=$groups,
833 #else
834 groups=None,
835 #end if 759 #end if
836 ]]></token> 760 ]]></token>
837 <xml name="pl_components"> 761 <xml name="pl_components">
838 <repeat name="components" title="Component"> 762 <repeat name="components" title="Component">
839 <param argument="axis1" type="text" value="1" label="Axis 1" help=""/> 763 <param argument="axis1" type="text" value="1" label="Axis 1" help=""/>
845 #set $components=[] 769 #set $components=[]
846 #for $i, $s in enumerate($method.plot.components) 770 #for $i, $s in enumerate($method.plot.components)
847 #silent $components.append(str($s.axis1) + ',' + str($s.axis2)) 771 #silent $components.append(str($s.axis1) + ',' + str($s.axis2))
848 #end for 772 #end for
849 components=$components, 773 components=$components,
850 #else
851 components=None,
852 #end if 774 #end if
853 ]]> 775 ]]>
854 </token> 776 </token>
855 <xml name="param_projection"> 777 <xml name="param_projection">
856 <param argument="projection" type="select" label="Projection of plot" help=""> 778 <param argument="projection" type="select" label="Projection of plot" help="">
875 <option value="upper center">upper center</option> 797 <option value="upper center">upper center</option>
876 <option value="center">center</option> 798 <option value="center">center</option>
877 </param> 799 </param>
878 </xml> 800 </xml>
879 <xml name="param_legend_fontsize"> 801 <xml name="param_legend_fontsize">
880 <param argument="legend_fontsize" type="integer" min="0" value="1" label="Legend font size" help=""/> 802 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size" help=""/>
881 </xml> 803 </xml>
882 <xml name="param_legend_fontweight"> 804 <xml name="param_legend_fontweight">
883 <param argument="legend_fontweight" type="select" label="Legend font weight" help=""> 805 <param argument="legend_fontweight" type="select" label="Legend font weight" help="">
884 <option value="light">light</option> 806 <option value="light">light</option>
885 <option value="normal" selected="true">normal</option> 807 <option value="normal" selected="true">normal</option>
908 </xml> 830 </xml>
909 <xml name="param_left_margin"> 831 <xml name="param_left_margin">
910 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/> 832 <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel" help=""/>
911 </xml> 833 </xml>
912 <xml name="param_size"> 834 <xml name="param_size">
913 <param argument="size" type="float" value="1" label="Point size" help=""/> 835 <param argument="size" type="float" optional="true" value="" label="Point size" help=""/>
914 </xml> 836 </xml>
915 <xml name="param_title"> 837 <xml name="param_title">
916 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/> 838 <param argument="title" type="text" value="" optional="true" label="Title for panels" help="Titles must be separated by a comma"/>
917 </xml> 839 </xml>
918 <xml name="param_sort_order"> 840 <xml name="param_sort_order">
935 <param argument="edges" type="select" label="Show edges?"> 857 <param argument="edges" type="select" label="Show edges?">
936 <option value="True">Yes</option> 858 <option value="True">Yes</option>
937 <option value="False" selected="true">No</option> 859 <option value="False" selected="true">No</option>
938 </param> 860 </param>
939 <when value="True"> 861 <when value="True">
940 <param name="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> 862 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
941 <param name="edges_color" type="select" label="Color of edges"> 863 <param argument="edges_color" type="select" label="Color of edges">
942 <expand macro="matplotlib_color"/> 864 <expand macro="matplotlib_color"/>
943 </param> 865 </param>
944 </when> 866 </when>
945 <when value="False"/> 867 <when value="False"/>
946 </conditional> 868 </conditional>
954 edges=False, 876 edges=False,
955 #end if 877 #end if
956 ]]> 878 ]]>
957 </token> 879 </token>
958 <xml name="param_arrows"> 880 <xml name="param_arrows">
959 <param name="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/> 881 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run `tl.rna_velocity` before."/>
960 </xml> 882 </xml>
961 <xml name="param_cmap"> 883 <xml name="param_cmap">
962 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 884 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
963 <expand macro="matplotlib_pyplot_colormap"/> 885 <expand macro="matplotlib_pyplot_colormap"/>
964 </param> 886 </param>
980 </section> 902 </section>
981 </xml> 903 </xml>
982 <token name="@CMD_pl_attribute_section@"><![CDATA[ 904 <token name="@CMD_pl_attribute_section@"><![CDATA[
983 projection='$method.plot.projection', 905 projection='$method.plot.projection',
984 legend_loc='$method.plot.legend_loc', 906 legend_loc='$method.plot.legend_loc',
907 #if str($method.plot.legend_fontsize) != ''
985 legend_fontsize=$method.plot.legend_fontsize, 908 legend_fontsize=$method.plot.legend_fontsize,
909 #end if
986 legend_fontweight='$method.plot.legend_fontweight', 910 legend_fontweight='$method.plot.legend_fontweight',
911 #if str($method.plot.size) != ''
987 size=$method.plot.size, 912 size=$method.plot.size,
913 #end if
988 palette='$method.plot.palette', 914 palette='$method.plot.palette',
989 frameon=$method.plot.frameon, 915 frameon=$method.plot.frameon,
990 ncols=$method.plot.ncols, 916 ncols=$method.plot.ncols,
991 wspace=$method.plot.wspace, 917 wspace=$method.plot.wspace,
992 hspace=$method.plot.hspace, 918 hspace=$method.plot.hspace,
993 #if $method.plot.title 919 #if $method.plot.title
994 title='$method.plot.title', 920 title='$method.plot.title',
995 #end if 921 #end if
996 ]]> 922 ]]>
997 </token> 923 </token>
924 <xml name="options_layout">
925 <option value="fa">fa: ForceAtlas2</option>
926 <option value="fr">fr: Fruchterman-Reingold</option>
927 <option value="grid_fr">grid_fr: Grid Fruchterman Reingold, faster than "fr"</option>
928 <option value="kk">kk: Kamadi Kawai’, slower than "fr"</option>
929 <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
930 <option value="rt">rt: Reingold Tilford tree layout</option>
931 <option value="eq_tree">eq_tree: Equally spaced tree</option>
932 </xml>
933 <xml name="param_layout">
934 <param argument="layout" type="select" label="Plotting layout" help="">
935 <expand macro="options_layout"/>
936 </param>
937 </xml>
938 <xml name="param_root">
939 <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."/>
940 </xml>
941 <xml name="param_random_state">
942 <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."/>
943 </xml>
998 <xml name="inputs_paga"> 944 <xml name="inputs_paga">
999 <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."/> 945 <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."/>
1000 <expand macro="pl_groups"/> 946 <expand macro="pl_groups"/>
1001 <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'."/> 947 <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'."/>
1002 <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=""/> 948 <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=""/>
1003 <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."/> 949 <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."/>
1004 <param argument="layout" type="select" value="" label="Plotting layout" help=""> 950 <expand macro="param_layout"/>
1005 <option value="fa">fa: ForceAtlas2</option>
1006 <option value="fr">fr: Fruchterman-Reingold</option>
1007 <option value="fr">rt: stands for Reingold Tilford</option>
1008 <option value="fr">eq_tree: equally spaced tree</option>
1009 </param>
1010 <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=""/> 951 <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=""/>
1011 <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."/> 952 <expand macro="param_random_state"/>
1012 <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."/> 953 <expand macro="param_root"/>
1013 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/> 954 <param argument="transitions" type="text" value="" label="Key corresponding to the matrix storing the arrows" help="Key for `.uns['paga']`, e.g. 'transistions_confidence'"/>
1014 <param argument="solid_edges" type="text" value="paga_connectivities" label="Key corresponding to the matrix storing the edges to be drawn solid black" help="Key for `.uns['paga']`"/> 955 <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"/>
1015 <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."/> 956 <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."/>
1016 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/> 957 <param argument="single_component" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Restrict to largest connected component?" help=""/>
1017 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/> 958 <param argument="fontsize" type="integer" min="0" value="1" label="Font size for node labels" help=""/>
1018 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/> 959 <param argument="node_size_scale" type="float" min="0" value="1.0" label="Size of the nodes" help=""/>
1019 <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=""/> 960 <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=""/>
1020 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/> 961 <param argument="edge_width_scale" type="float" min="0" value="5" label="Scale for edge width" help=""/>
1029 <token name="@CMD_params_pl_paga@"><![CDATA[ 970 <token name="@CMD_params_pl_paga@"><![CDATA[
1030 threshold=$method.threshold, 971 threshold=$method.threshold,
1031 #if str($method.groups) != '' 972 #if str($method.groups) != ''
1032 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 973 #set $groups=([x.strip() for x in str($method.groups).split(',')])
1033 groups=$groups, 974 groups=$groups,
1034 #else 975 #end if
1035 groups=None, 976 #if str($method.color) != ''
1036 #end if 977 #set $color=([x.strip() for x in str($method.color).split(',')])
1037 color='$method.color', 978 color=$color,
979 #end if
1038 #if $method.pos 980 #if $method.pos
1039 pos=np.fromfile($method.pos, dtype=dt), 981 pos=np.fromfile($method.pos, dtype=dt),
1040 #end if 982 #end if
1041 #if str($method.labels) != '' 983 #if str($method.labels) != ''
1042 #set $labels=([x.strip() for x in str($method.labels).split(',')]) 984 #set $labels=([x.strip() for x in str($method.labels).split(',')])
1079 ]]> 1021 ]]>
1080 </token> 1022 </token>
1081 <xml name="param_swap_axes"> 1023 <xml name="param_swap_axes">
1082 <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`."/> 1024 <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`."/>
1083 </xml> 1025 </xml>
1026 <xml name="gene_symbols">
1027 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in `.var` that stores gene symbols"/>
1028 </xml>
1029 <xml name="n_genes">
1030 <param argument="n_genes" type="integer" min="0" value="20" label="Number of genes to show" help=""/>
1031 </xml>
1084 </macros> 1032 </macros>