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comparison macros.xml @ 12:9b0cdb8cf6be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0
author iuc
date Fri, 17 Nov 2023 09:14:28 +0000
parents 95777145cb92
children 6f5349dd5c49
comparison
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11:95777145cb92 12:9b0cdb8cf6be
1 <macros> 1 <macros>
2 <token name="@version@">1.9.6</token> 2 <token name="@TOOL_VERSION@">1.9.6</token>
3 <token name="@VERSION_SUFFIX@">1</token>
3 <token name="@profile@">22.05</token> 4 <token name="@profile@">22.05</token>
4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></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="@TOOL_VERSION@">scanpy</requirement>
8 <requirement type="package" version="3.0.6">loompy</requirement> 8 <requirement type="package" version="3.0.6">loompy</requirement>
9 <requirement type="package" version="0.10.1">leidenalg</requirement> 9 <requirement type="package" version="0.10.1">leidenalg</requirement>
10 <requirement type="package" version="0.8.1">louvain</requirement> 10 <requirement type="package" version="0.8.1">louvain</requirement>
11 <requirement type="package" version="1.5.3">pandas</requirement> 11 <requirement type="package" version="1.5.3">pandas</requirement>
12 <requirement type="package" version="3.7">matplotlib</requirement> 12 <requirement type="package" version="3.7">matplotlib</requirement>
467 <expand macro="param_num_categories"/> 467 <expand macro="param_num_categories"/>
468 </xml> 468 </xml>
469 <token name="@CMD_params_inputs@"><![CDATA[ 469 <token name="@CMD_params_inputs@"><![CDATA[
470 #if $method.var_names.type == 'all' 470 #if $method.var_names.type == 'all'
471 var_names=adata.var_names, 471 var_names=adata.var_names,
472 #else 472 #else
473 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) 473 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
474 var_names=$var_names, 474 var_names=$var_names,
475 #end if 475 #end if
476 #if str($method.groupby) != '' 476 #if $method.groupby
477 groupby='$method.groupby', 477 groupby='$method.groupby',
478 #end if 478 #end if
479 num_categories=$method.num_categories, 479 num_categories=$method.num_categories,
480 ]]></token> 480 ]]></token>
481 <xml name="params_plots"> 481 <xml name="params_plots">
482 <expand macro="param_log"/> 482 <expand macro="param_log"/>
483 <expand macro="param_use_raw"/> 483 <expand macro="param_use_raw"/>
499 #silent $var_group_labels.append(str($s.label)) 499 #silent $var_group_labels.append(str($s.label))
500 #end for 500 #end for
501 var_group_positions=$var_group_positions, 501 var_group_positions=$var_group_positions,
502 var_group_labels=$var_group_labels, 502 var_group_labels=$var_group_labels,
503 #end if 503 #end if
504 #if $method.var_group_rotation 504 #if str($method.var_group_rotation) != ''
505 var_group_rotation=$method.var_group_rotation, 505 var_group_rotation=$method.var_group_rotation,
506 #end if 506 #end if
507 #if $method.figsize.test == 'yes' 507 #if $method.figsize.test == 'yes'
508 figsize=($method.figsize.width, $method.figsize.height), 508 figsize=($method.figsize.width, $method.figsize.height),
509 #end if 509 #end if
510 #if $method.layer != '' 510 #if $method.layer
511 layer='$method.layer', 511 layer='$method.layer',
512 #end if 512 #end if
513 ]]></token> 513 ]]></token>
514 <xml name="matplotlib_color"> 514 <xml name="matplotlib_color">
515 <option value="AliceBlue">AliceBlue</option> 515 <option value="AliceBlue">AliceBlue</option>
516 <option value="AntiqueWhite">AntiqueWhite</option> 516 <option value="AntiqueWhite">AntiqueWhite</option>
517 <option value="Aqua">Aqua</option> 517 <option value="Aqua">Aqua</option>
660 <option value="WhiteSmoke">WhiteSmoke</option> 660 <option value="WhiteSmoke">WhiteSmoke</option>
661 <option value="Yellow">Yellow</option> 661 <option value="Yellow">Yellow</option>
662 <option value="YellowGreen">YellowGreen</option> 662 <option value="YellowGreen">YellowGreen</option>
663 </xml> 663 </xml>
664 <xml name="param_matplotlib_pyplot_edgecolors"> 664 <xml name="param_matplotlib_pyplot_edgecolors">
665 <param argument="edgecolors" type="select" label="Edge color of the marker" help=""> 665 <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
666 <option value="face">The edge color will always be the same as the face color</option> 666 <option value="face">The edge color will always be the same as the face color</option>
667 <option value="none">No patch boundary will be drawn</option>
668 <expand macro="matplotlib_color"/> 667 <expand macro="matplotlib_color"/>
669 </param> 668 </param>
670 </xml> 669 </xml>
671 <xml name="param_alpha"> 670 <xml name="param_alpha">
672 <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/> 671 <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/>
700 <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/> 699 <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/>
701 <expand macro="param_matplotlib_pyplot_edgecolors"/> 700 <expand macro="param_matplotlib_pyplot_edgecolors"/>
702 </section> 701 </section>
703 </xml> 702 </xml>
704 <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[ 703 <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
705 #if $method.matplotlib_pyplot_scatter.vmin 704 #if str($method.matplotlib_pyplot_scatter.vmin) != ''
706 vmin=$method.matplotlib_pyplot_scatter.vmin, 705 vmin=$method.matplotlib_pyplot_scatter.vmin,
707 #end if 706 #end if
708 #if $method.matplotlib_pyplot_scatter.vmax 707 #if str($method.matplotlib_pyplot_scatter.vmax) != ''
709 vmax=$method.matplotlib_pyplot_scatter.vmax, 708 vmax=$method.matplotlib_pyplot_scatter.vmax,
710 #end if 709 #end if
711 #if $method.matplotlib_pyplot_scatter.alpha 710 #if str($method.matplotlib_pyplot_scatter.alpha) != ''
712 alpha=$method.matplotlib_pyplot_scatter.alpha, 711 alpha=$method.matplotlib_pyplot_scatter.alpha,
713 #end if 712 #end if
714 linewidths=$method.matplotlib_pyplot_scatter.linewidths, 713 lw=$method.matplotlib_pyplot_scatter.linewidths,
715 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' 714 #if $method.matplotlib_pyplot_scatter.edgecolors
715 ec='$method.matplotlib_pyplot_scatter.edgecolors'
716 #end if
716 ]]></token> 717 ]]></token>
717 <xml name="conditional_stripplot"> 718 <xml name="conditional_stripplot">
718 <conditional name="stripplot"> 719 <conditional name="stripplot">
719 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help=""> 720 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
720 <option value="True">Yes</option> 721 <option value="True">Yes</option>
750 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option> 751 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
751 <option value="width" selected="true">width: each violin will have the same width</option> 752 <option value="width" selected="true">width: each violin will have the same width</option>
752 </param> 753 </param>
753 </xml> 754 </xml>
754 <token name="@CMD_params_violin_plots@"><![CDATA[ 755 <token name="@CMD_params_violin_plots@"><![CDATA[
755 stripplot=$method.violin_plot.stripplot.stripplot, 756 @CMD_conditional_stripplot@
756 #if $method.violin_plot.stripplot.stripplot == "True"
757 jitter=$method.violin_plot.stripplot.jitter.jitter,
758 #if $method.violin_plot.stripplot.jitter.jitter == "True"
759 size=$method.violin_plot.stripplot.jitter.size,
760 #end if
761 #end if
762 multi_panel=$method.violin_plot.multi_panel.multi_panel, 757 multi_panel=$method.violin_plot.multi_panel.multi_panel,
763 #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) != '' 758 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
764 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) 759 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
765 #end if 760 #end if
766 scale='$method.violin_plot.scale', 761 scale='$method.violin_plot.scale',
774 <param argument="orient" type="select" optional="true" label="Orientation of the plot"> 769 <param argument="orient" type="select" optional="true" label="Orientation of the plot">
775 <option value="v">vertical</option> 770 <option value="v">vertical</option>
776 <option value="h">horizontal</option> 771 <option value="h">horizontal</option>
777 </param> 772 </param>
778 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/> 773 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
779 <param argument="color" type="select" label="Color for all of the elements" help=""> 774 <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
780 <expand macro="matplotlib_color"/> 775 <expand macro="matplotlib_color"/>
781 </param> 776 </param>
782 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> 777 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
783 </section> 778 </section>
784 </xml> 779 </xml>
786 bw='$method.seaborn_violinplot.bw', 781 bw='$method.seaborn_violinplot.bw',
787 #if $method.seaborn_violinplot.orient 782 #if $method.seaborn_violinplot.orient
788 orient='$method.seaborn_violinplot.orient', 783 orient='$method.seaborn_violinplot.orient',
789 #end if 784 #end if
790 linewidth=$method.seaborn_violinplot.linewidth, 785 linewidth=$method.seaborn_violinplot.linewidth,
786 #if $method.seaborn_violinplot.color
791 color='$method.seaborn_violinplot.color', 787 color='$method.seaborn_violinplot.color',
788 #end if
792 saturation=$method.seaborn_violinplot.saturation 789 saturation=$method.seaborn_violinplot.saturation
793 ]]></token> 790 ]]></token>
794 <xml name="param_color"> 791 <xml name="param_color">
795 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"> 792 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
796 <expand macro="sanitize_query" /> 793 <expand macro="sanitize_query" />
797 </param> 794 </param>
798 </xml> 795 </xml>
799 <token name="@CMD_param_color@"><![CDATA[ 796 <token name="@CMD_param_color@"><![CDATA[
800 #if str($method.color) != '' 797 #if $method.color
801 #set $color = ([x.strip() for x in str($method.color).split(',')]) 798 #set $color = ([x.strip() for x in str($method.color).split(',')])
802 color=$color, 799 color=$color,
803 #end if 800 #end if
804 ]]></token> 801 ]]></token>
805 <xml name="param_groups"> 802 <xml name="param_groups">
806 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"> 803 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
807 <expand macro="sanitize_query" /> 804 <expand macro="sanitize_query" />
808 </param> 805 </param>
809 </xml> 806 </xml>
810 <token name="@CMD_params_groups@"><![CDATA[ 807 <token name="@CMD_params_groups@"><![CDATA[
811 #if str($method.groups) != '' 808 #if $method.groups
812 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 809 #set $groups=([x.strip() for x in str($method.groups).split(',')])
813 groups=$groups, 810 groups=$groups,
814 #end if 811 #end if
815 ]]></token> 812 ]]></token>
816 <xml name="pl_components"> 813 <xml name="pl_components">
876 <option value="heavy">heavy</option> 873 <option value="heavy">heavy</option>
877 <option value="black">black</option> 874 <option value="black">black</option>
878 </param> 875 </param>
879 </xml> 876 </xml>
880 <xml name="param_palette"> 877 <xml name="param_palette">
881 <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 878 <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
882 <option value="default">Default</option>
883 <expand macro="matplotlib_pyplot_colormap"/> 879 <expand macro="matplotlib_pyplot_colormap"/>
884 </param> 880 </param>
885 </xml> 881 </xml>
886 <xml name="param_color_map"> 882 <xml name="param_color_map">
887 <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> 883 <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
888 <option value="" >Default</option>
889 <expand macro="matplotlib_pyplot_colormap"/> 884 <expand macro="matplotlib_pyplot_colormap"/>
890 </param> 885 </param>
891 </xml> 886 </xml>
892 <xml name="param_frameon"> 887 <xml name="param_frameon">
893 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/> 888 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
939 <option value="True">Yes</option> 934 <option value="True">Yes</option>
940 <option value="False" selected="true">No</option> 935 <option value="False" selected="true">No</option>
941 </param> 936 </param>
942 <when value="True"> 937 <when value="True">
943 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> 938 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
944 <param argument="edges_color" type="select" label="Color of edges"> 939 <param argument="edges_color" type="select" optional="true" label="Color of edges">
945 <expand macro="matplotlib_color"/> 940 <expand macro="matplotlib_color"/>
946 </param> 941 </param>
947 </when> 942 </when>
948 <when value="False"/> 943 <when value="False"/>
949 </conditional> 944 </conditional>
950 </xml> 945 </xml>
951 <token name="@CMD_pl_edges@"><![CDATA[ 946 <token name="@CMD_pl_edges@"><![CDATA[
952 #if str($method.edges.edges) == 'True' 947 #if str($method.edges.edges) == 'True'
953 edges=True, 948 edges=True,
954 edges_width=$method.edges.edges_width, 949 edges_width=$method.edges.edges_width,
950 #if $method.edges.edges_color
955 edges_color='$method.edges.edges_color', 951 edges_color='$method.edges.edges_color',
952 #end if
956 #else 953 #else
957 edges=False, 954 edges=False,
958 #end if 955 #end if
959 ]]> 956 ]]>
960 </token> 957 </token>
961 <xml name="param_arrows"> 958 <xml name="param_arrows">
962 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/> 959 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
963 </xml> 960 </xml>
964 <xml name="param_cmap"> 961 <xml name="param_cmap">
965 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 962 <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
966 <expand macro="matplotlib_pyplot_colormap"/> 963 <expand macro="matplotlib_pyplot_colormap"/>
967 </param> 964 </param>
968 </xml> 965 </xml>
969 <xml name="pl_attribute_section"> 966 <xml name="pl_attribute_section">
970 <section name="plot" title="Plot attributes"> 967 <section name="plot" title="Plot attributes">
987 projection='$method.plot.projection', 984 projection='$method.plot.projection',
988 legend_loc='$method.plot.legend_loc', 985 legend_loc='$method.plot.legend_loc',
989 @CMD_param_legend_fontsize@ 986 @CMD_param_legend_fontsize@
990 legend_fontweight='$method.plot.legend_fontweight', 987 legend_fontweight='$method.plot.legend_fontweight',
991 @CMD_param_size@ 988 @CMD_param_size@
992 #if str($method.plot.color_map) != '' 989 #if $method.plot.color_map
993 color_map='$method.plot.color_map', 990 color_map='$method.plot.color_map',
994 #end if 991 #end if
995 #if str($method.plot.palette) != '' 992 #if $method.plot.palette
996 palette='$method.plot.palette', 993 palette='$method.plot.palette',
997 #end if 994 #end if
998 frameon=$method.plot.frameon, 995 frameon=$method.plot.frameon,
999 ncols=$method.plot.ncols, 996 ncols=$method.plot.ncols,
1000 wspace=$method.plot.wspace, 997 wspace=$method.plot.wspace,
1060 <expand macro="param_title"/> 1057 <expand macro="param_title"/>
1061 <expand macro="param_frameon"/> 1058 <expand macro="param_frameon"/>
1062 </xml> 1059 </xml>
1063 <token name="@CMD_params_pl_paga@"><![CDATA[ 1060 <token name="@CMD_params_pl_paga@"><![CDATA[
1064 threshold=$method.threshold, 1061 threshold=$method.threshold,
1065 #if str($method.groups) != '' 1062 #if $method.groups
1066 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 1063 #set $groups=([x.strip() for x in str($method.groups).split(',')])
1067 groups=$groups, 1064 groups=$groups,
1068 #end if 1065 #end if
1069 #if str($method.color) != '' 1066 #if $method.color
1070 #set $color=([x.strip() for x in str($method.color).split(',')]) 1067 #set $color=([x.strip() for x in str($method.color).split(',')])
1071 color=$color, 1068 color=$color,
1072 #end if 1069 #end if
1073 #if $method.pos 1070 #if $method.pos
1074 pos=np.fromfile($method.pos, dtype=dt), 1071 pos=np.fromfile($method.pos, dtype=dt),
1075 #end if 1072 #end if
1076 #if str($method.labels) != '' 1073 #if $method.labels
1077 #set $labels=([x.strip() for x in str($method.labels).split(',')]) 1074 #set $labels=([x.strip() for x in str($method.labels).split(',')])
1078 labels=$labels, 1075 labels=$labels,
1079 #end if 1076 #end if
1080 layout='$method.layout', 1077 layout='$method.layout',
1081 #if $method.init_pos 1078 #if $method.init_pos
1082 init_pos=np.fromfile($method.init_pos, dtype=dt), 1079 init_pos=np.fromfile($method.init_pos, dtype=dt),
1083 #end if 1080 #end if
1084 random_state=$method.random_state, 1081 random_state=$method.random_state,
1085 #if str($method.root) != '' 1082 #if $method.root
1086 #set $root=([int(x.strip()) for x in str($method.root).split(',')]) 1083 #set $root=([int(x.strip()) for x in str($method.root).split(',')])
1087 root=$root, 1084 root=$root,
1088 #end if 1085 #end if
1089 #if $method.transitions 1086 #if $method.transitions
1090 transitions='$method.transitions', 1087 transitions='$method.transitions',
1096 single_component=$method.single_component, 1093 single_component=$method.single_component,
1097 fontsize=$method.fontsize, 1094 fontsize=$method.fontsize,
1098 node_size_scale=$method.node_size_scale, 1095 node_size_scale=$method.node_size_scale,
1099 node_size_power=$method.node_size_power, 1096 node_size_power=$method.node_size_power,
1100 edge_width_scale=$method.edge_width_scale, 1097 edge_width_scale=$method.edge_width_scale,
1101 #if $method.min_edge_width 1098 #if str($method.min_edge_width) != ''
1102 min_edge_width=$method.min_edge_width, 1099 min_edge_width=$method.min_edge_width,
1103 #end if 1100 #end if
1104 #if $method.max_edge_width 1101 #if str($method.max_edge_width) != ''
1105 max_edge_width=$method.max_edge_width, 1102 max_edge_width=$method.max_edge_width,
1106 #end if 1103 #end if
1107 arrowsize=$method.arrowsize, 1104 arrowsize=$method.arrowsize,
1108 normalize_to_color=$method.normalize_to_color, 1105 normalize_to_color=$method.normalize_to_color,
1106 #if $method.cmap
1109 cmap='$method.cmap', 1107 cmap='$method.cmap',
1108 #end if
1110 #if $method.title 1109 #if $method.title
1111 title='$method.title', 1110 title='$method.title',
1112 #end if 1111 #end if
1113 frameon=$method.frameon, 1112 frameon=$method.frameon,
1114 ]]> 1113 ]]>
1123 </xml> 1122 </xml>
1124 <xml name="param_n_genes"> 1123 <xml name="param_n_genes">
1125 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> 1124 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
1126 </xml> 1125 </xml>
1127 <xml name="pl_dotplot"> 1126 <xml name="pl_dotplot">
1128 <param argument="color_map" type="select" label="Color palette"> 1127 <param argument="color_map" type="select" optional="true" label="Color palette">
1129 <expand macro="matplotlib_pyplot_colormap"/> 1128 <expand macro="matplotlib_pyplot_colormap"/>
1130 </param> 1129 </param>
1131 <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."/> 1130 <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."/>
1132 <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."/> 1131 <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."/>
1133 <expand macro="section_matplotlib_pyplot_scatter"/> 1132 <expand macro="section_matplotlib_pyplot_scatter"/>
1134 </xml> 1133 </xml>
1135 <token name="@CMD_pl_dotplot@"><![CDATA[ 1134 <token name="@CMD_pl_dotplot@"><![CDATA[
1135 #if $method.color_map
1136 color_map='$method.color_map', 1136 color_map='$method.color_map',
1137 #end if
1137 #if str($method.dot_max) != '' 1138 #if str($method.dot_max) != ''
1138 dot_max=$method.dot_max, 1139 dot_max=$method.dot_max,
1139 #end if 1140 #end if
1140 #if str($method.dot_min) != '' 1141 #if str($method.dot_min) != ''
1141 dot_min=$method.dot_min, 1142 dot_min=$method.dot_min,
1182 </section> 1183 </section>
1183 </xml> 1184 </xml>
1184 <token name="@CMD_pl_heatmap@"><![CDATA[ 1185 <token name="@CMD_pl_heatmap@"><![CDATA[
1185 swap_axes=$method.swap_axes, 1186 swap_axes=$method.swap_axes,
1186 show_gene_labels=$method.show_gene_labels, 1187 show_gene_labels=$method.show_gene_labels,
1188 #if $method.matplotlib_pyplot_imshow.cmap
1187 cmap='$method.matplotlib_pyplot_imshow.cmap', 1189 cmap='$method.matplotlib_pyplot_imshow.cmap',
1190 #end if
1188 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None' 1191 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
1189 interpolation='$method.matplotlib_pyplot_imshow.interpolation', 1192 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
1190 #end if 1193 #end if
1191 #if $method.matplotlib_pyplot_imshow.alpha 1194 #if str($method.matplotlib_pyplot_imshow.alpha) != ''
1192 alpha=$method.matplotlib_pyplot_imshow.alpha, 1195 alpha=$method.matplotlib_pyplot_imshow.alpha,
1193 #end if 1196 #end if
1194 #if $method.matplotlib_pyplot_imshow.vmin 1197 #if str($method.matplotlib_pyplot_imshow.vmin) != ''
1195 vmin=$method.matplotlib_pyplot_imshow.vmin, 1198 vmin=$method.matplotlib_pyplot_imshow.vmin,
1196 #end if 1199 #end if
1197 #if $method.matplotlib_pyplot_imshow.vmax 1200 #if str($method.matplotlib_pyplot_imshow.vmax) != ''
1198 vmax=$method.matplotlib_pyplot_imshow.vmax, 1201 vmax=$method.matplotlib_pyplot_imshow.vmax,
1199 #end if 1202 #end if
1200 origin='$method.matplotlib_pyplot_imshow.origin' 1203 origin='$method.matplotlib_pyplot_imshow.origin'
1201 ]]> 1204 ]]>
1202 </token> 1205 </token>
1205 <expand macro="param_n_genes"/> 1208 <expand macro="param_n_genes"/>
1206 <expand macro="param_key"/> 1209 <expand macro="param_key"/>
1207 </xml> 1210 </xml>
1208 <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[ 1211 <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
1209 @CMD_params_groups@ 1212 @CMD_params_groups@
1210 #if str($method.n_genes) != ''
1211 n_genes=$method.n_genes, 1213 n_genes=$method.n_genes,
1212 #end if 1214 #if $method.key
1213 #if str($method.key) != ''
1214 key='$method.key', 1215 key='$method.key',
1215 #end if 1216 #end if
1216 ]]> 1217 ]]>
1217 </token> 1218 </token>
1218 <xml name="pl_matrixplot"> 1219 <xml name="pl_matrixplot">
1219 <expand macro="param_swap_axes"/> 1220 <expand macro="param_swap_axes"/>
1220 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor"> 1221 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
1221 <param argument="cmap" type="select" label="Color palette"> 1222 <param argument="cmap" type="select" optional="true" label="Color palette">
1222 <expand macro="seaborn_color_palette_options"/> 1223 <expand macro="seaborn_color_palette_options"/>
1223 </param> 1224 </param>
1224 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/> 1225 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
1225 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/> 1226 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
1226 <expand macro="param_matplotlib_pyplot_edgecolors"/> 1227 <expand macro="param_matplotlib_pyplot_edgecolors"/>
1228 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/> 1229 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
1229 </section> 1230 </section>
1230 </xml> 1231 </xml>
1231 <token name="@CMD_pl_matrixplot@"><![CDATA[ 1232 <token name="@CMD_pl_matrixplot@"><![CDATA[
1232 swap_axes=$method.swap_axes, 1233 swap_axes=$method.swap_axes,
1234 #if $method.matplotlib_pyplot_pcolor.cmap
1233 cmap='$method.matplotlib_pyplot_pcolor.cmap', 1235 cmap='$method.matplotlib_pyplot_pcolor.cmap',
1234 #if $method.matplotlib_pyplot_pcolor.vmin 1236 #end if
1237 #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
1235 vmin=$method.matplotlib_pyplot_pcolor.vmin, 1238 vmin=$method.matplotlib_pyplot_pcolor.vmin,
1236 #end if 1239 #end if
1237 #if $method.matplotlib_pyplot_pcolor.vmax 1240 #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
1238 vmax=$method.matplotlib_pyplot_pcolor.vmax, 1241 vmax=$method.matplotlib_pyplot_pcolor.vmax,
1239 #end if 1242 #end if
1240 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors', 1243 #if $method.matplotlib_pyplot_pcolor.edgecolors
1241 #if $method.matplotlib_pyplot_pcolor.alpha 1244 ec='$method.matplotlib_pyplot_pcolor.edgecolors',
1245 #end if
1246 #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
1242 alpha=$method.matplotlib_pyplot_pcolor.alpha, 1247 alpha=$method.matplotlib_pyplot_pcolor.alpha,
1243 #end if 1248 #end if
1244 snap=$method.matplotlib_pyplot_pcolor.snap 1249 snap=$method.matplotlib_pyplot_pcolor.snap
1245 ]]> 1250 ]]>
1246 </token> 1251 </token>
1248 <expand macro="param_swap_axes"/> 1253 <expand macro="param_swap_axes"/>
1249 <section name="violin_plot" title="Violin plot attributes"> 1254 <section name="violin_plot" title="Violin plot attributes">
1250 <expand macro="conditional_stripplot"/> 1255 <expand macro="conditional_stripplot"/>
1251 <expand macro="param_scale"/> 1256 <expand macro="param_scale"/>
1252 </section> 1257 </section>
1253 <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots"> 1258 <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
1254 <option value="muted">muted</option> 1259 <option value="muted">muted</option>
1255 <expand macro="seaborn_color_palette_options"/> 1260 <expand macro="seaborn_color_palette_options"/>
1256 </param> 1261 </param>
1257 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum."> 1262 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
1258 <option value="None">No standardization</option> 1263 <option value="None">No standardization</option>
1263 </xml> 1268 </xml>
1264 <token name="@CMD_pl_stacked_violin@"><![CDATA[ 1269 <token name="@CMD_pl_stacked_violin@"><![CDATA[
1265 swap_axes=$method.swap_axes, 1270 swap_axes=$method.swap_axes,
1266 @CMD_conditional_stripplot@ 1271 @CMD_conditional_stripplot@
1267 scale='$method.violin_plot.scale', 1272 scale='$method.violin_plot.scale',
1273 #if $method.row_palette
1268 row_palette='$method.row_palette', 1274 row_palette='$method.row_palette',
1275 #end if
1269 #if str($method.standard_scale) != 'None' 1276 #if str($method.standard_scale) != 'None'
1270 standard_scale='$method.standard_scale', 1277 standard_scale='$method.standard_scale',
1271 #end if 1278 #end if
1272 @CMD_params_seaborn_violinplot@ 1279 @CMD_params_seaborn_violinplot@
1273 ]]> 1280 ]]>