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comparison macros.xml @ 12:1f380e8a6aec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0
author iuc
date Wed, 31 Jul 2024 18:07:15 +0000
parents 69a12ab93cdd
children 084c74890a1f
comparison
equal deleted inserted replaced
11:69a12ab93cdd 12:1f380e8a6aec
1 <macros> 1 <macros>
2 <token name="@version@">1.7.1</token> 2 <token name="@TOOL_VERSION@">1.9.6</token>
3 <token name="@profile@">19.01</token> 3 <token name="@VERSION_SUFFIX@">4</token>
4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> 4 <token name="@profile@">21.09</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="2.0.17">loompy</requirement> 8 <requirement type="package" version="3.0.6">loompy</requirement>
9 <requirement type="package" version="0.8.3">leidenalg</requirement> 9 <requirement type="package" version="0.10.1">leidenalg</requirement>
10 <requirement type="package" version="0.8.1">louvain</requirement>
11 <requirement type="package" version="1.5.3">pandas</requirement>
12 <requirement type="package" version="3.7">matplotlib</requirement>
13 <requirement type="package" version="0.12.2">seaborn</requirement>
14 <requirement type="package" version="3.0.0">magic-impute</requirement>
10 <yield /> 15 <yield />
11 </requirements> 16 </requirements>
12 </xml> 17 </xml>
13 <xml name="bio_tools"> 18 <xml name="bio_tools">
14 <xrefs> 19 <xrefs>
15 <xref type="bio.tools">scanpy</xref> 20 <xref type="bio.tools">scanpy</xref>
16 </xrefs> 21 </xrefs>
17 </xml> 22 </xml>
23 <xml name="creators">
24 <creator>
25 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
26 </creator>
27 </xml>
18 <xml name="citations"> 28 <xml name="citations">
19 <citations> 29 <citations>
20 <citation type="doi">10.1186/s13059-017-1382-0</citation> 30 <citation type="doi">10.1186/s13059-017-1382-0</citation>
31 <citation type="doi">10.1093/gigascience/giaa102</citation>
21 </citations> 32 </citations>
22 </xml> 33 </xml>
23 <xml name="version_command"> 34 <xml name="version_command">
24 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> 35 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
25 </xml> 36 </xml>
54 </xml> 65 </xml>
55 <xml name="inputs_anndata"> 66 <xml name="inputs_anndata">
56 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> 67 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
57 </xml> 68 </xml>
58 <token name="@CMD_read_inputs@"><![CDATA[ 69 <token name="@CMD_read_inputs@"><![CDATA[
59 adata = sc.read('anndata.h5ad') 70 adata = sc.read_h5ad('anndata.h5ad')
60 ]]> 71 ]]>
61 </token> 72 </token>
62 <xml name="inputs_common_advanced"> 73 <xml name="inputs_common_advanced">
63 <section name="advanced_common" title="Advanced Options" expanded="false"> 74 <section name="advanced_common" title="Advanced Options" expanded="false">
64 <param name="show_log" type="boolean" checked="false" label="Output Log?" /> 75 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
65 </section> 76 </section>
66 </xml> 77 </xml>
67 <xml name="anndata_outputs"> 78 <xml name="anndata_outputs">
68 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> 79 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
69 <data name="hidden_output" format="txt" label="Log file" > 80 <data name="hidden_output" format="txt" label="Log file" >
70 <filter>advanced_common['show_log']</filter> 81 <filter>advanced_common['show_log']</filter>
71 </data> 82 </data>
72 </xml> 83 </xml>
73 <token name="@CMD_anndata_write_outputs@"><![CDATA[ 84 <token name="@CMD_anndata_write_outputs@"><![CDATA[
74 adata.write('anndata.h5ad') 85 adata.write_h5ad('anndata.h5ad')
75 with open('anndata_info.txt','w', encoding='utf-8') as ainfo: 86 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
76 print(adata, file=ainfo) 87 print(adata, file=ainfo)
77 ]]> 88 ]]>
78 </token> 89 </token>
79 <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g' 90 <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g'
412 <xml name="pl_var_names"> 423 <xml name="pl_var_names">
413 <conditional name="var_names"> 424 <conditional name="var_names">
414 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" > 425 <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
415 <option value="all">All variables in 'adata.var_names'</option> 426 <option value="all">All variables in 'adata.var_names'</option>
416 <option value="custom">Subset of variables in 'adata.var_names'</option> 427 <option value="custom">Subset of variables in 'adata.var_names'</option>
428 <option value="customfile">Subset of variables as a tabular file</option>
417 </param> 429 </param>
418 <when value="all"/> 430 <when value="all"/>
419 <when value="custom"> 431 <when value="custom">
420 <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"> 432 <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">
421 <expand macro="sanitize_query" /> 433 <expand macro="sanitize_query" />
422 </param> 434 </param>
435 </when>
436 <when value="customfile">
437 <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
423 </when> 438 </when>
424 </conditional> 439 </conditional>
425 </xml> 440 </xml>
426 <xml name="param_num_categories"> 441 <xml name="param_num_categories">
427 <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."/> 442 <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."/>
455 <expand macro="pl_var_names"/> 470 <expand macro="pl_var_names"/>
456 <expand macro="param_groupby"/> 471 <expand macro="param_groupby"/>
457 <expand macro="param_num_categories"/> 472 <expand macro="param_num_categories"/>
458 </xml> 473 </xml>
459 <token name="@CMD_params_inputs@"><![CDATA[ 474 <token name="@CMD_params_inputs@"><![CDATA[
460 #if $method.var_names.type == 'all' 475 #if $method.var_names.type == 'custom'
461 var_names=adata.var_names,
462 #else
463 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) 476 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
464 var_names=$var_names, 477 var_names=$var_names,
465 #end if 478 #else if $method.var_names.type == 'customfile'
466 #if str($method.groupby) != '' 479 var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
480 #else
481 var_names=adata.var_names,
482 #end if
483 #if $method.groupby
467 groupby='$method.groupby', 484 groupby='$method.groupby',
468 #end if 485 #end if
469 num_categories=$method.num_categories, 486 num_categories=$method.num_categories,
470 ]]></token> 487 ]]></token>
471 <xml name="params_plots"> 488 <xml name="params_plots">
472 <expand macro="param_log"/> 489 <expand macro="param_log"/>
473 <expand macro="param_use_raw"/> 490 <expand macro="param_use_raw"/>
489 #silent $var_group_labels.append(str($s.label)) 506 #silent $var_group_labels.append(str($s.label))
490 #end for 507 #end for
491 var_group_positions=$var_group_positions, 508 var_group_positions=$var_group_positions,
492 var_group_labels=$var_group_labels, 509 var_group_labels=$var_group_labels,
493 #end if 510 #end if
494 #if $method.var_group_rotation 511 #if str($method.var_group_rotation) != ''
495 var_group_rotation=$method.var_group_rotation, 512 var_group_rotation=$method.var_group_rotation,
496 #end if 513 #end if
497 #if $method.figsize.test == 'yes' 514 #if $method.figsize.test == 'yes'
498 figsize=($method.figsize.width, $method.figsize.height), 515 figsize=($method.figsize.width, $method.figsize.height),
499 #end if 516 #end if
500 #if $method.layer != '' 517 #if $method.layer
501 layer='$method.layer', 518 layer='$method.layer',
502 #end if 519 #end if
503 ]]></token> 520 ]]></token>
504 <xml name="matplotlib_color"> 521 <xml name="matplotlib_color">
505 <option value="AliceBlue">AliceBlue</option> 522 <option value="AliceBlue">AliceBlue</option>
506 <option value="AntiqueWhite">AntiqueWhite</option> 523 <option value="AntiqueWhite">AntiqueWhite</option>
507 <option value="Aqua">Aqua</option> 524 <option value="Aqua">Aqua</option>
650 <option value="WhiteSmoke">WhiteSmoke</option> 667 <option value="WhiteSmoke">WhiteSmoke</option>
651 <option value="Yellow">Yellow</option> 668 <option value="Yellow">Yellow</option>
652 <option value="YellowGreen">YellowGreen</option> 669 <option value="YellowGreen">YellowGreen</option>
653 </xml> 670 </xml>
654 <xml name="param_matplotlib_pyplot_edgecolors"> 671 <xml name="param_matplotlib_pyplot_edgecolors">
655 <param argument="edgecolors" type="select" label="Edge color of the marker" help=""> 672 <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
656 <option value="face">The edge color will always be the same as the face color</option> 673 <option value="face">The edge color will always be the same as the face color</option>
657 <option value="none">No patch boundary will be drawn</option>
658 <expand macro="matplotlib_color"/> 674 <expand macro="matplotlib_color"/>
659 </param> 675 </param>
660 </xml> 676 </xml>
661 <xml name="param_alpha"> 677 <xml name="param_alpha">
662 <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/> 678 <param argument="alpha" type="float" value="" min="0" max="1" optional="true" label="Alpha blending value" help="Between 0 (transparent) and 1 (opaque)"/>
690 <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/> 706 <param argument="linewidths" type="float" value="0" label="Linewidth of the marker edges" help=""/>
691 <expand macro="param_matplotlib_pyplot_edgecolors"/> 707 <expand macro="param_matplotlib_pyplot_edgecolors"/>
692 </section> 708 </section>
693 </xml> 709 </xml>
694 <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[ 710 <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
695 #if $method.matplotlib_pyplot_scatter.vmin 711 #if str($method.matplotlib_pyplot_scatter.vmin) != ''
696 vmin=$method.matplotlib_pyplot_scatter.vmin, 712 vmin=$method.matplotlib_pyplot_scatter.vmin,
697 #end if 713 #end if
698 #if $method.matplotlib_pyplot_scatter.vmax 714 #if str($method.matplotlib_pyplot_scatter.vmax) != ''
699 vmax=$method.matplotlib_pyplot_scatter.vmax, 715 vmax=$method.matplotlib_pyplot_scatter.vmax,
700 #end if 716 #end if
701 #if $method.matplotlib_pyplot_scatter.alpha 717 #if str($method.matplotlib_pyplot_scatter.alpha) != ''
702 alpha=$method.matplotlib_pyplot_scatter.alpha, 718 alpha=$method.matplotlib_pyplot_scatter.alpha,
703 #end if 719 #end if
704 linewidths=$method.matplotlib_pyplot_scatter.linewidths, 720 lw=$method.matplotlib_pyplot_scatter.linewidths,
705 edgecolors='$method.matplotlib_pyplot_scatter.edgecolors' 721 #if $method.matplotlib_pyplot_scatter.edgecolors
722 ec='$method.matplotlib_pyplot_scatter.edgecolors'
723 #end if
706 ]]></token> 724 ]]></token>
707 <xml name="conditional_stripplot"> 725 <xml name="conditional_stripplot">
708 <conditional name="stripplot"> 726 <conditional name="stripplot">
709 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help=""> 727 <param argument="stripplot" type="select" label="Add a stripplot on top of the violin plot" help="">
710 <option value="True">Yes</option> 728 <option value="True">Yes</option>
740 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option> 758 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
741 <option value="width" selected="true">width: each violin will have the same width</option> 759 <option value="width" selected="true">width: each violin will have the same width</option>
742 </param> 760 </param>
743 </xml> 761 </xml>
744 <token name="@CMD_params_violin_plots@"><![CDATA[ 762 <token name="@CMD_params_violin_plots@"><![CDATA[
745 stripplot=$method.violin_plot.stripplot.stripplot, 763 @CMD_conditional_stripplot@
746 #if $method.violin_plot.stripplot.stripplot == "True"
747 jitter=$method.violin_plot.stripplot.jitter.jitter,
748 #if $method.violin_plot.stripplot.jitter.jitter == "True"
749 size=$method.violin_plot.stripplot.jitter.size,
750 #end if
751 #end if
752 multi_panel=$method.violin_plot.multi_panel.multi_panel, 764 multi_panel=$method.violin_plot.multi_panel.multi_panel,
753 #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) != '' 765 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
754 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height) 766 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
755 #end if 767 #end if
756 scale='$method.violin_plot.scale', 768 scale='$method.violin_plot.scale',
764 <param argument="orient" type="select" optional="true" label="Orientation of the plot"> 776 <param argument="orient" type="select" optional="true" label="Orientation of the plot">
765 <option value="v">vertical</option> 777 <option value="v">vertical</option>
766 <option value="h">horizontal</option> 778 <option value="h">horizontal</option>
767 </param> 779 </param>
768 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/> 780 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
769 <param argument="color" type="select" label="Color for all of the elements" help=""> 781 <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
770 <expand macro="matplotlib_color"/> 782 <expand macro="matplotlib_color"/>
771 </param> 783 </param>
772 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> 784 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
773 </section> 785 </section>
774 </xml> 786 </xml>
776 bw='$method.seaborn_violinplot.bw', 788 bw='$method.seaborn_violinplot.bw',
777 #if $method.seaborn_violinplot.orient 789 #if $method.seaborn_violinplot.orient
778 orient='$method.seaborn_violinplot.orient', 790 orient='$method.seaborn_violinplot.orient',
779 #end if 791 #end if
780 linewidth=$method.seaborn_violinplot.linewidth, 792 linewidth=$method.seaborn_violinplot.linewidth,
793 #if $method.seaborn_violinplot.color
781 color='$method.seaborn_violinplot.color', 794 color='$method.seaborn_violinplot.color',
795 #end if
782 saturation=$method.seaborn_violinplot.saturation 796 saturation=$method.seaborn_violinplot.saturation
783 ]]></token> 797 ]]></token>
784 <xml name="param_color"> 798 <xml name="param_color">
785 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"> 799 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
786 <expand macro="sanitize_query" /> 800 <expand macro="sanitize_query" />
787 </param> 801 </param>
788 </xml> 802 </xml>
789 <token name="@CMD_param_color@"><![CDATA[ 803 <token name="@CMD_param_color@"><![CDATA[
790 #if str($method.color) != '' 804 #if $method.color
791 #set $color = ([x.strip() for x in str($method.color).split(',')]) 805 #set $color = ([x.strip() for x in str($method.color).split(',')])
792 color=$color, 806 color=$color,
793 #end if 807 #end if
794 ]]></token> 808 ]]></token>
795 <xml name="param_groups"> 809 <xml name="param_groups">
796 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated"> 810 <param argument="groups" type="text" value="" optional="true" label="Categorical observation annotations to plot" help="Comma-separated">
797 <expand macro="sanitize_query" /> 811 <expand macro="sanitize_query" />
798 </param> 812 </param>
799 </xml> 813 </xml>
800 <token name="@CMD_params_groups@"><![CDATA[ 814 <token name="@CMD_params_groups@"><![CDATA[
801 #if str($method.groups) != '' 815 #if $method.groups
802 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 816 #set $groups=([x.strip() for x in str($method.groups).split(',')])
803 groups=$groups, 817 groups=$groups,
804 #end if 818 #end if
805 ]]></token> 819 ]]></token>
806 <xml name="pl_components"> 820 <xml name="pl_components">
866 <option value="heavy">heavy</option> 880 <option value="heavy">heavy</option>
867 <option value="black">black</option> 881 <option value="black">black</option>
868 </param> 882 </param>
869 </xml> 883 </xml>
870 <xml name="param_palette"> 884 <xml name="param_palette">
871 <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 885 <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
872 <option value="default">Default</option>
873 <expand macro="matplotlib_pyplot_colormap"/> 886 <expand macro="matplotlib_pyplot_colormap"/>
874 </param> 887 </param>
875 </xml> 888 </xml>
876 <xml name="param_color_map"> 889 <xml name="param_color_map">
877 <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> 890 <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
878 <option value="None">Default</option>
879 <expand macro="matplotlib_pyplot_colormap"/> 891 <expand macro="matplotlib_pyplot_colormap"/>
880 </param> 892 </param>
881 </xml> 893 </xml>
882 <xml name="param_frameon"> 894 <xml name="param_frameon">
883 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/> 895 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
929 <option value="True">Yes</option> 941 <option value="True">Yes</option>
930 <option value="False" selected="true">No</option> 942 <option value="False" selected="true">No</option>
931 </param> 943 </param>
932 <when value="True"> 944 <when value="True">
933 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/> 945 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
934 <param argument="edges_color" type="select" label="Color of edges"> 946 <param argument="edges_color" type="select" optional="true" label="Color of edges">
935 <expand macro="matplotlib_color"/> 947 <expand macro="matplotlib_color"/>
936 </param> 948 </param>
937 </when> 949 </when>
938 <when value="False"/> 950 <when value="False"/>
939 </conditional> 951 </conditional>
940 </xml> 952 </xml>
941 <token name="@CMD_pl_edges@"><![CDATA[ 953 <token name="@CMD_pl_edges@"><![CDATA[
942 #if str($method.edges.edges) == 'True' 954 #if str($method.edges.edges) == 'True'
943 edges=True, 955 edges=True,
944 edges_width=$method.edges.edges_width, 956 edges_width=$method.edges.edges_width,
957 #if $method.edges.edges_color
945 edges_color='$method.edges.edges_color', 958 edges_color='$method.edges.edges_color',
959 #end if
946 #else 960 #else
947 edges=False, 961 edges=False,
948 #end if 962 #end if
949 ]]> 963 ]]>
950 </token> 964 </token>
951 <xml name="param_arrows"> 965 <xml name="param_arrows">
952 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/> 966 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
953 </xml> 967 </xml>
954 <xml name="param_cmap"> 968 <xml name="param_cmap">
955 <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help=""> 969 <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
956 <expand macro="matplotlib_pyplot_colormap"/> 970 <expand macro="matplotlib_pyplot_colormap"/>
957 </param> 971 </param>
958 </xml> 972 </xml>
959 <xml name="pl_attribute_section"> 973 <xml name="pl_attribute_section">
960 <section name="plot" title="Plot attributes"> 974 <section name="plot" title="Plot attributes">
977 projection='$method.plot.projection', 991 projection='$method.plot.projection',
978 legend_loc='$method.plot.legend_loc', 992 legend_loc='$method.plot.legend_loc',
979 @CMD_param_legend_fontsize@ 993 @CMD_param_legend_fontsize@
980 legend_fontweight='$method.plot.legend_fontweight', 994 legend_fontweight='$method.plot.legend_fontweight',
981 @CMD_param_size@ 995 @CMD_param_size@
982 #if str($method.plot.color_map) != 'None' 996 #if $method.plot.color_map
983 color_map='$method.plot.color_map', 997 color_map='$method.plot.color_map',
984 #end if 998 #end if
985 #if str($method.plot.palette) != '' 999 #if $method.plot.palette
986 palette='$method.plot.palette', 1000 palette='$method.plot.palette',
987 #end if 1001 #end if
988 frameon=$method.plot.frameon, 1002 frameon=$method.plot.frameon,
989 ncols=$method.plot.ncols, 1003 ncols=$method.plot.ncols,
990 wspace=$method.plot.wspace, 1004 wspace=$method.plot.wspace,
1050 <expand macro="param_title"/> 1064 <expand macro="param_title"/>
1051 <expand macro="param_frameon"/> 1065 <expand macro="param_frameon"/>
1052 </xml> 1066 </xml>
1053 <token name="@CMD_params_pl_paga@"><![CDATA[ 1067 <token name="@CMD_params_pl_paga@"><![CDATA[
1054 threshold=$method.threshold, 1068 threshold=$method.threshold,
1055 #if str($method.groups) != '' 1069 #if $method.groups
1056 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 1070 #set $groups=([x.strip() for x in str($method.groups).split(',')])
1057 groups=$groups, 1071 groups=$groups,
1058 #end if 1072 #end if
1059 #if str($method.color) != '' 1073 #if $method.color
1060 #set $color=([x.strip() for x in str($method.color).split(',')]) 1074 #set $color=([x.strip() for x in str($method.color).split(',')])
1061 color=$color, 1075 color=$color,
1062 #end if 1076 #end if
1063 #if $method.pos 1077 #if $method.pos
1064 pos=np.fromfile($method.pos, dtype=dt), 1078 pos=np.fromfile($method.pos, dtype=dt),
1065 #end if 1079 #end if
1066 #if str($method.labels) != '' 1080 #if $method.labels
1067 #set $labels=([x.strip() for x in str($method.labels).split(',')]) 1081 #set $labels=([x.strip() for x in str($method.labels).split(',')])
1068 labels=$labels, 1082 labels=$labels,
1069 #end if 1083 #end if
1070 layout='$method.layout', 1084 layout='$method.layout',
1071 #if $method.init_pos 1085 #if $method.init_pos
1072 init_pos=np.fromfile($method.init_pos, dtype=dt), 1086 init_pos=np.fromfile($method.init_pos, dtype=dt),
1073 #end if 1087 #end if
1074 random_state=$method.random_state, 1088 random_state=$method.random_state,
1075 #if str($method.root) != '' 1089 #if $method.root
1076 #set $root=([int(x.strip()) for x in str($method.root).split(',')]) 1090 #set $root=([int(x.strip()) for x in str($method.root).split(',')])
1077 root=$root, 1091 root=$root,
1078 #end if 1092 #end if
1079 #if $method.transitions 1093 #if $method.transitions
1080 transitions='$method.transitions', 1094 transitions='$method.transitions',
1086 single_component=$method.single_component, 1100 single_component=$method.single_component,
1087 fontsize=$method.fontsize, 1101 fontsize=$method.fontsize,
1088 node_size_scale=$method.node_size_scale, 1102 node_size_scale=$method.node_size_scale,
1089 node_size_power=$method.node_size_power, 1103 node_size_power=$method.node_size_power,
1090 edge_width_scale=$method.edge_width_scale, 1104 edge_width_scale=$method.edge_width_scale,
1091 #if $method.min_edge_width 1105 #if str($method.min_edge_width) != ''
1092 min_edge_width=$method.min_edge_width, 1106 min_edge_width=$method.min_edge_width,
1093 #end if 1107 #end if
1094 #if $method.max_edge_width 1108 #if str($method.max_edge_width) != ''
1095 max_edge_width=$method.max_edge_width, 1109 max_edge_width=$method.max_edge_width,
1096 #end if 1110 #end if
1097 arrowsize=$method.arrowsize, 1111 arrowsize=$method.arrowsize,
1098 normalize_to_color=$method.normalize_to_color, 1112 normalize_to_color=$method.normalize_to_color,
1113 #if $method.cmap
1099 cmap='$method.cmap', 1114 cmap='$method.cmap',
1115 #end if
1100 #if $method.title 1116 #if $method.title
1101 title='$method.title', 1117 title='$method.title',
1102 #end if 1118 #end if
1103 frameon=$method.frameon, 1119 frameon=$method.frameon,
1104 ]]> 1120 ]]>
1110 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols"> 1126 <param argument="gene_symbols" type="text" value="" optional="true" label="Key for field in '.var' that stores gene symbols">
1111 <expand macro="sanitize_query" /> 1127 <expand macro="sanitize_query" />
1112 </param> 1128 </param>
1113 </xml> 1129 </xml>
1114 <xml name="param_n_genes"> 1130 <xml name="param_n_genes">
1115 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/> 1131 <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
1116 </xml> 1132 </xml>
1117 <xml name="pl_dotplot"> 1133 <xml name="pl_dotplot">
1118 <param argument="color_map" type="select" label="Color palette"> 1134 <param argument="color_map" type="select" optional="true" label="Color palette">
1119 <expand macro="matplotlib_pyplot_colormap"/> 1135 <expand macro="matplotlib_pyplot_colormap"/>
1120 </param> 1136 </param>
1121 <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."/> 1137 <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."/>
1122 <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."/> 1138 <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."/>
1123 <expand macro="section_matplotlib_pyplot_scatter"/> 1139 <expand macro="section_matplotlib_pyplot_scatter"/>
1124 </xml> 1140 </xml>
1125 <token name="@CMD_pl_dotplot@"><![CDATA[ 1141 <token name="@CMD_pl_dotplot@"><![CDATA[
1142 #if $method.color_map
1126 color_map='$method.color_map', 1143 color_map='$method.color_map',
1144 #end if
1127 #if str($method.dot_max) != '' 1145 #if str($method.dot_max) != ''
1128 dot_max=$method.dot_max, 1146 dot_max=$method.dot_max,
1129 #end if 1147 #end if
1130 #if str($method.dot_min) != '' 1148 #if str($method.dot_min) != ''
1131 dot_min=$method.dot_min, 1149 dot_min=$method.dot_min,
1172 </section> 1190 </section>
1173 </xml> 1191 </xml>
1174 <token name="@CMD_pl_heatmap@"><![CDATA[ 1192 <token name="@CMD_pl_heatmap@"><![CDATA[
1175 swap_axes=$method.swap_axes, 1193 swap_axes=$method.swap_axes,
1176 show_gene_labels=$method.show_gene_labels, 1194 show_gene_labels=$method.show_gene_labels,
1195 #if $method.matplotlib_pyplot_imshow.cmap
1177 cmap='$method.matplotlib_pyplot_imshow.cmap', 1196 cmap='$method.matplotlib_pyplot_imshow.cmap',
1197 #end if
1178 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None' 1198 #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
1179 interpolation='$method.matplotlib_pyplot_imshow.interpolation', 1199 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
1180 #end if 1200 #end if
1181 #if $method.matplotlib_pyplot_imshow.alpha 1201 #if str($method.matplotlib_pyplot_imshow.alpha) != ''
1182 alpha=$method.matplotlib_pyplot_imshow.alpha, 1202 alpha=$method.matplotlib_pyplot_imshow.alpha,
1183 #end if 1203 #end if
1184 #if $method.matplotlib_pyplot_imshow.vmin 1204 #if str($method.matplotlib_pyplot_imshow.vmin) != ''
1185 vmin=$method.matplotlib_pyplot_imshow.vmin, 1205 vmin=$method.matplotlib_pyplot_imshow.vmin,
1186 #end if 1206 #end if
1187 #if $method.matplotlib_pyplot_imshow.vmax 1207 #if str($method.matplotlib_pyplot_imshow.vmax) != ''
1188 vmax=$method.matplotlib_pyplot_imshow.vmax, 1208 vmax=$method.matplotlib_pyplot_imshow.vmax,
1189 #end if 1209 #end if
1190 origin='$method.matplotlib_pyplot_imshow.origin' 1210 origin='$method.matplotlib_pyplot_imshow.origin'
1191 ]]> 1211 ]]>
1192 </token> 1212 </token>
1195 <expand macro="param_n_genes"/> 1215 <expand macro="param_n_genes"/>
1196 <expand macro="param_key"/> 1216 <expand macro="param_key"/>
1197 </xml> 1217 </xml>
1198 <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[ 1218 <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
1199 @CMD_params_groups@ 1219 @CMD_params_groups@
1200 #if str($method.n_genes) != ''
1201 n_genes=$method.n_genes, 1220 n_genes=$method.n_genes,
1202 #end if 1221 #if $method.key
1203 #if str($method.key) != ''
1204 key='$method.key', 1222 key='$method.key',
1205 #end if 1223 #end if
1206 ]]> 1224 ]]>
1207 </token> 1225 </token>
1208 <xml name="pl_matrixplot"> 1226 <xml name="pl_matrixplot">
1209 <expand macro="param_swap_axes"/> 1227 <expand macro="param_swap_axes"/>
1210 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor"> 1228 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
1211 <param argument="cmap" type="select" label="Color palette"> 1229 <param argument="cmap" type="select" optional="true" label="Color palette">
1212 <expand macro="seaborn_color_palette_options"/> 1230 <expand macro="seaborn_color_palette_options"/>
1213 </param> 1231 </param>
1214 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/> 1232 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
1215 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/> 1233 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
1216 <expand macro="param_matplotlib_pyplot_edgecolors"/> 1234 <expand macro="param_matplotlib_pyplot_edgecolors"/>
1218 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/> 1236 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
1219 </section> 1237 </section>
1220 </xml> 1238 </xml>
1221 <token name="@CMD_pl_matrixplot@"><![CDATA[ 1239 <token name="@CMD_pl_matrixplot@"><![CDATA[
1222 swap_axes=$method.swap_axes, 1240 swap_axes=$method.swap_axes,
1241 #if $method.matplotlib_pyplot_pcolor.cmap
1223 cmap='$method.matplotlib_pyplot_pcolor.cmap', 1242 cmap='$method.matplotlib_pyplot_pcolor.cmap',
1224 #if $method.matplotlib_pyplot_pcolor.vmin 1243 #end if
1244 #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
1225 vmin=$method.matplotlib_pyplot_pcolor.vmin, 1245 vmin=$method.matplotlib_pyplot_pcolor.vmin,
1226 #end if 1246 #end if
1227 #if $method.matplotlib_pyplot_pcolor.vmax 1247 #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
1228 vmax=$method.matplotlib_pyplot_pcolor.vmax, 1248 vmax=$method.matplotlib_pyplot_pcolor.vmax,
1229 #end if 1249 #end if
1230 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors', 1250 #if $method.matplotlib_pyplot_pcolor.edgecolors
1231 #if $method.matplotlib_pyplot_pcolor.alpha 1251 ec='$method.matplotlib_pyplot_pcolor.edgecolors',
1252 #end if
1253 #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
1232 alpha=$method.matplotlib_pyplot_pcolor.alpha, 1254 alpha=$method.matplotlib_pyplot_pcolor.alpha,
1233 #end if 1255 #end if
1234 snap=$method.matplotlib_pyplot_pcolor.snap 1256 snap=$method.matplotlib_pyplot_pcolor.snap
1235 ]]> 1257 ]]>
1236 </token> 1258 </token>
1238 <expand macro="param_swap_axes"/> 1260 <expand macro="param_swap_axes"/>
1239 <section name="violin_plot" title="Violin plot attributes"> 1261 <section name="violin_plot" title="Violin plot attributes">
1240 <expand macro="conditional_stripplot"/> 1262 <expand macro="conditional_stripplot"/>
1241 <expand macro="param_scale"/> 1263 <expand macro="param_scale"/>
1242 </section> 1264 </section>
1243 <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots"> 1265 <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
1244 <option value="muted">muted</option> 1266 <option value="muted">muted</option>
1245 <expand macro="seaborn_color_palette_options"/> 1267 <expand macro="seaborn_color_palette_options"/>
1246 </param> 1268 </param>
1247 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum."> 1269 <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">
1248 <option value="None">No standardization</option> 1270 <option value="None">No standardization</option>
1253 </xml> 1275 </xml>
1254 <token name="@CMD_pl_stacked_violin@"><![CDATA[ 1276 <token name="@CMD_pl_stacked_violin@"><![CDATA[
1255 swap_axes=$method.swap_axes, 1277 swap_axes=$method.swap_axes,
1256 @CMD_conditional_stripplot@ 1278 @CMD_conditional_stripplot@
1257 scale='$method.violin_plot.scale', 1279 scale='$method.violin_plot.scale',
1280 #if $method.row_palette
1258 row_palette='$method.row_palette', 1281 row_palette='$method.row_palette',
1282 #end if
1259 #if str($method.standard_scale) != 'None' 1283 #if str($method.standard_scale) != 'None'
1260 standard_scale='$method.standard_scale', 1284 standard_scale='$method.standard_scale',
1261 #end if 1285 #end if
1262 @CMD_params_seaborn_violinplot@ 1286 @CMD_params_seaborn_violinplot@
1263 ]]> 1287 ]]>