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comparison plot.xml @ 6:dbbe1ea8ecb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:22:46 -0500
parents 8599fd07d140
children 7647e5cd1b8b
comparison
equal deleted inserted replaced
5:8599fd07d140 6:dbbe1ea8ecb1
80 groupby='$method.groupby', 80 groupby='$method.groupby',
81 #end if 81 #end if
82 log=$method.log, 82 log=$method.log,
83 use_raw=$method.use_raw, 83 use_raw=$method.use_raw,
84 @CMD_conditional_stripplot@ 84 @CMD_conditional_stripplot@
85 multi_panel=$method.violin_plot.multi_panel.multi_panel, 85 multi_panel=$method.violin_plot.multi_panel.multi_panel,
86 #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != '' 86 #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
87 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height), 87 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
88 #end if 88 #end if
89 scale='$method.violin_plot.scale', 89 scale='$method.violin_plot.scale',
90 #if $method.xlabel 90 #if $method.xlabel
549 <section name="setseaborn_boxplot" title="Plot settings" expanded="false"> 549 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
550 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/> 550 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
551 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details."> 551 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
552 <expand macro="seaborn_color_palette_options"/> 552 <expand macro="seaborn_color_palette_options"/>
553 </param> 553 </param>
554 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/> 554 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
555 </section> 555 </section>
556 </when> 556 </when>
557 <when value="pl.pca"> 557 <when value="pl.pca">
558 <expand macro="param_color"/> 558 <expand macro="param_color"/>
559 <expand macro="param_use_raw"/> 559 <expand macro="param_use_raw"/>
639 </when> 639 </when>
640 <when value="pl.paga_compare"> 640 <when value="pl.paga_compare">
641 <expand macro="inputs_paga"/> 641 <expand macro="inputs_paga"/>
642 </when> 642 </when>
643 <when value="pl.paga_path"> 643 <when value="pl.paga_path">
644 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" 644 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
645 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/> 645 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated"/>
646 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/> 646 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'"/>
647 <expand macro="param_use_raw"/> 647 <expand macro="param_use_raw"/>
648 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/> 648 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated"/>
649 <expand macro="param_color_map"/> 649 <expand macro="param_color_map"/>
704 <expand macro="pl_rank_genes_groups_ext"/> 704 <expand macro="pl_rank_genes_groups_ext"/>
705 <expand macro="params_plots"/> 705 <expand macro="params_plots"/>
706 <expand macro="pl_stacked_violin"/> 706 <expand macro="pl_stacked_violin"/>
707 </when> 707 </when>
708 </conditional> 708 </conditional>
709 <expand macro="inputs_common_advanced"/>
709 </inputs> 710 </inputs>
710 <outputs> 711 <outputs>
711 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}"> 712 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} (${method.method}) on ${on_string}">
712 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter> 713 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
713 </data> 714 </data>
727 </data> 728 </data>
728 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}"> 729 <collection name="collection_svg" type="list" label="${tool.name} (${method.method}) on ${on_string}">
729 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/> 730 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
730 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 731 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
731 </collection> 732 </collection>
733 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
734 <filter>advanced_common['show_log']</filter>
735 </data>
732 </outputs> 736 </outputs>
733 <tests> 737 <tests>
734 <test> 738 <test>
735 <!-- test 1: pl.scatter !--> 739 <!-- test 0: pl.scatter !-->
736 <param name="adata" value="pbmc68k_reduced.h5ad" /> 740 <param name="adata" value="pbmc68k_reduced.h5ad" />
737 <param name="format" value="png"/> 741 <param name="format" value="png"/>
738 <conditional name="method"> 742 <conditional name="method">
739 <param name="method" value="pl.scatter"/> 743 <param name="method" value="pl.scatter"/>
740 <conditional name="type"> 744 <conditional name="type">
753 <param name="palette" value="inferno"/> 757 <param name="palette" value="inferno"/>
754 <param name="frameon" value="True"/> 758 <param name="frameon" value="True"/>
755 <param name="size" value="1"/> 759 <param name="size" value="1"/>
756 </section> 760 </section>
757 </conditional> 761 </conditional>
758 <assert_stdout> 762 <section name="advanced_common">
759 <has_text_matching expression="sc.pl.scatter"/> 763 <param name="show_log" value="true" />
760 <has_text_matching expression="basis='umap'" /> 764 </section>
761 <has_text_matching expression="color=\['HES4'\]"/> 765 <output name="hidden_output">
762 <has_text_matching expression="use_raw=True"/> 766 <assert_contents>
763 <has_text_matching expression="sort_order=True"/> 767 <has_text_matching expression="sc.pl.scatter"/>
764 <has_text_matching expression="projection='2d'"/> 768 <has_text_matching expression="basis='umap'" />
765 <has_text_matching expression="legend_loc='right margin'"/> 769 <has_text_matching expression="color=\['HES4'\]"/>
766 <has_text_matching expression="legend_fontsize=1"/> 770 <has_text_matching expression="use_raw=True"/>
767 <has_text_matching expression="legend_fontweight='normal'"/> 771 <has_text_matching expression="sort_order=True"/>
768 <has_text_matching expression="color_map='inferno'"/> 772 <has_text_matching expression="projection='2d'"/>
769 <has_text_matching expression="palette='inferno'"/> 773 <has_text_matching expression="legend_loc='right margin'"/>
770 <has_text_matching expression="frameon=True"/> 774 <has_text_matching expression="legend_fontsize=1"/>
771 <has_text_matching expression="size=1.0"/> 775 <has_text_matching expression="legend_fontweight='normal'"/>
772 </assert_stdout> 776 <has_text_matching expression="color_map='inferno'"/>
777 <has_text_matching expression="palette='inferno'"/>
778 <has_text_matching expression="frameon=True"/>
779 <has_text_matching expression="size=1.0"/>
780 </assert_contents>
781 </output>
773 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> 782 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
774 </test> 783 </test>
775 <test> 784 <test>
776 <!-- test 2: pl.scatter !--> 785 <!-- test 1: pl.scatter !-->
777 <param name="adata" value="krumsiek11.h5ad" /> 786 <param name="adata" value="krumsiek11.h5ad" />
778 <param name="format" value="png"/> 787 <param name="format" value="png"/>
779 <conditional name="method"> 788 <conditional name="method">
780 <param name="method" value="pl.scatter"/> 789 <param name="method" value="pl.scatter"/>
781 <conditional name="type"> 790 <conditional name="type">
797 <param name="frameon" value="False"/> 806 <param name="frameon" value="False"/>
798 <param name="size" value="1"/> 807 <param name="size" value="1"/>
799 <param name="title" value="A title"/> 808 <param name="title" value="A title"/>
800 </section> 809 </section>
801 </conditional> 810 </conditional>
802 <assert_stdout> 811 <section name="advanced_common">
803 <has_text_matching expression="sc.pl.scatter"/> 812 <param name="show_log" value="true" />
804 <has_text_matching expression="x='EKLF'" /> 813 </section>
805 <has_text_matching expression="y='Cebpa'"/> 814 <output name="hidden_output">
806 <has_text_matching expression="use_raw=False"/> 815 <assert_contents>
807 <has_text_matching expression="sort_order=True"/> 816 <has_text_matching expression="sc.pl.scatter"/>
808 <has_text_matching expression="projection='2d'"/> 817 <has_text_matching expression="x='EKLF'" />
809 <has_text_matching expression="legend_loc='right margin'"/> 818 <has_text_matching expression="y='Cebpa'"/>
810 <has_text_matching expression="legend_fontsize=1"/> 819 <has_text_matching expression="use_raw=False"/>
811 <has_text_matching expression="legend_fontweight='normal'"/> 820 <has_text_matching expression="sort_order=True"/>
812 <has_text_matching expression="palette='bwr'"/> 821 <has_text_matching expression="projection='2d'"/>
813 <has_text_matching expression="frameon=False"/> 822 <has_text_matching expression="legend_loc='right margin'"/>
814 <has_text_matching expression="size=1.0"/> 823 <has_text_matching expression="legend_fontsize=1"/>
815 <has_text_matching expression="title='A title'"/> 824 <has_text_matching expression="legend_fontweight='normal'"/>
816 </assert_stdout> 825 <has_text_matching expression="palette='bwr'"/>
826 <has_text_matching expression="frameon=False"/>
827 <has_text_matching expression="size=1.0"/>
828 <has_text_matching expression="title='A title'"/>
829 </assert_contents>
830 </output>
817 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/> 831 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
818 </test> 832 </test>
819 <test> 833 <test>
820 <!-- test 3: pl.heatmap !--> 834 <!-- test 2: pl.heatmap !-->
821 <param name="adata" value="krumsiek11.h5ad" /> 835 <param name="adata" value="krumsiek11.h5ad" />
822 <param name="format" value="png"/> 836 <param name="format" value="png"/>
823 <conditional name="method"> 837 <conditional name="method">
824 <param name="method" value="pl.heatmap"/> 838 <param name="method" value="pl.heatmap"/>
825 <conditional name="var_names"> 839 <conditional name="var_names">
841 <param name="cmap" value="YlGnBu"/> 855 <param name="cmap" value="YlGnBu"/>
842 <param name="interpolation" value="None"/> 856 <param name="interpolation" value="None"/>
843 <param name="origin" value="upper"/> 857 <param name="origin" value="upper"/>
844 </section> 858 </section>
845 </conditional> 859 </conditional>
846 <assert_stdout> 860 <section name="advanced_common">
847 <has_text_matching expression="sc.pl.heatmap"/> 861 <param name="show_log" value="true" />
848 <has_text_matching expression="var_names=adata.var_names" /> 862 </section>
849 <has_text_matching expression="groupby='cell_type'"/> 863 <output name="hidden_output">
850 <has_text_matching expression="log=False"/> 864 <assert_contents>
851 <has_text_matching expression="use_raw=False"/> 865 <has_text_matching expression="sc.pl.heatmap"/>
852 <has_text_matching expression="num_categories=7"/> 866 <has_text_matching expression="var_names=adata.var_names" />
853 <has_text_matching expression="dendrogram=True"/> 867 <has_text_matching expression="groupby='cell_type'"/>
854 <has_text_matching expression="figsize=\(10, 3\)"/> 868 <has_text_matching expression="log=False"/>
855 <has_text_matching expression="swap_axes=True"/> 869 <has_text_matching expression="use_raw=False"/>
856 <has_text_matching expression="show_gene_labels=False"/> 870 <has_text_matching expression="num_categories=7"/>
857 <has_text_matching expression="cmap='YlGnBu'"/> 871 <has_text_matching expression="dendrogram=True"/>
858 <has_text_matching expression="origin='upper'"/> 872 <has_text_matching expression="figsize=\(10, 3\)"/>
859 </assert_stdout> 873 <has_text_matching expression="swap_axes=True"/>
874 <has_text_matching expression="show_gene_labels=False"/>
875 <has_text_matching expression="cmap='YlGnBu'"/>
876 <has_text_matching expression="origin='upper'"/>
877 </assert_contents>
878 </output>
860 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/> 879 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
861 </test> 880 </test>
862 <test> 881 <test>
863 <!-- test 4: pl.dotplot !--> 882 <!-- test 3: pl.dotplot !-->
864 <param name="adata" value="pbmc68k_reduced.h5ad" /> 883 <param name="adata" value="pbmc68k_reduced.h5ad" />
865 <param name="format" value="png"/> 884 <param name="format" value="png"/>
866 <conditional name="method"> 885 <conditional name="method">
867 <param name="method" value="pl.dotplot"/> 886 <param name="method" value="pl.dotplot"/>
868 <conditional name="var_names"> 887 <conditional name="var_names">
893 <section name="matplotlib_pyplot_scatter"> 912 <section name="matplotlib_pyplot_scatter">
894 <param name="linewidths" value="0" /> 913 <param name="linewidths" value="0" />
895 <param name="edgecolors" value="face"/> 914 <param name="edgecolors" value="face"/>
896 </section> 915 </section>
897 </conditional> 916 </conditional>
898 <assert_stdout> 917 <section name="advanced_common">
899 <has_text_matching expression="sc.pl.dotplot"/> 918 <param name="show_log" value="true" />
900 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" /> 919 </section>
901 <has_text_matching expression="groupby='louvain'"/> 920 <output name="hidden_output">
902 <has_text_matching expression="log=False"/> 921 <assert_contents>
903 <has_text_matching expression="use_raw=False"/> 922 <has_text_matching expression="sc.pl.dotplot"/>
904 <has_text_matching expression="num_categories=7"/> 923 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
905 <has_text_matching expression="dendrogram=True"/> 924 <has_text_matching expression="groupby='louvain'"/>
906 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/> 925 <has_text_matching expression="log=False"/>
907 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/> 926 <has_text_matching expression="use_raw=False"/>
908 <has_text_matching expression="color_map='hot'"/> 927 <has_text_matching expression="num_categories=7"/>
909 <has_text_matching expression="dot_max=0.7"/> 928 <has_text_matching expression="dendrogram=True"/>
910 <has_text_matching expression="dot_min=0.1"/> 929 <has_text_matching expression="var_group_positions=\[\(0, 1\), \(11, 12\)\]"/>
911 <has_text_matching expression="linewidths=0.0"/> 930 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
912 <has_text_matching expression="edgecolors='face'"/> 931 <has_text_matching expression="color_map='hot'"/>
913 </assert_stdout> 932 <has_text_matching expression="dot_max=0.7"/>
933 <has_text_matching expression="dot_min=0.1"/>
934 <has_text_matching expression="linewidths=0.0"/>
935 <has_text_matching expression="edgecolors='face'"/>
936 </assert_contents>
937 </output>
914 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/> 938 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
915 </test> 939 </test>
916 <test> 940 <test>
917 <!-- test 5: pl.violin !--> 941 <!-- test 4: pl.violin !-->
918 <param name="adata" value="pbmc68k_reduced.h5ad" /> 942 <param name="adata" value="pbmc68k_reduced.h5ad" />
919 <param name="format" value="png"/> 943 <param name="format" value="png"/>
920 <conditional name="method"> 944 <conditional name="method">
921 <param name="method" value="pl.violin"/> 945 <param name="method" value="pl.violin"/>
922 <conditional name="key_variables"> 946 <conditional name="key_variables">
944 <param name="color" value="AliceBlue"/> 968 <param name="color" value="AliceBlue"/>
945 <param name="palette" value="viridis"/> 969 <param name="palette" value="viridis"/>
946 <param name="saturation" value="0.75"/> 970 <param name="saturation" value="0.75"/>
947 </section> 971 </section>
948 </conditional> 972 </conditional>
949 <assert_stdout> 973 <section name="advanced_common">
950 <has_text_matching expression="sc.pl.violin"/> 974 <param name="show_log" value="true" />
951 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" /> 975 </section>
952 <has_text_matching expression="log=False"/> 976 <output name="hidden_output">
953 <has_text_matching expression="use_raw=False"/> 977 <assert_contents>
954 <has_text_matching expression="stripplot=True"/> 978 <has_text_matching expression="sc.pl.violin"/>
955 <has_text_matching expression="jitter=True"/> 979 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
956 <has_text_matching expression="size=1"/> 980 <has_text_matching expression="log=False"/>
957 <has_text_matching expression="multi_panel=True"/> 981 <has_text_matching expression="use_raw=False"/>
958 <has_text_matching expression="figsize=\(20, 20\)"/> 982 <has_text_matching expression="stripplot=True"/>
959 <has_text_matching expression="scale='width'"/> 983 <has_text_matching expression="jitter=True"/>
960 <has_text_matching expression="bw='scott'"/> 984 <has_text_matching expression="size=1"/>
961 <has_text_matching expression="scale='width'"/> 985 <has_text_matching expression="multi_panel=True"/>
962 <has_text_matching expression="linewidth=0.0"/> 986 <has_text_matching expression="figsize=\(20, 20\)"/>
963 <has_text_matching expression="color='AliceBlue'"/> 987 <has_text_matching expression="scale='width'"/>
964 <has_text_matching expression="palette='viridis'"/> 988 <has_text_matching expression="bw='scott'"/>
965 <has_text_matching expression="saturation=0.75"/> 989 <has_text_matching expression="scale='width'"/>
966 </assert_stdout> 990 <has_text_matching expression="linewidth=0.0"/>
991 <has_text_matching expression="color='AliceBlue'"/>
992 <has_text_matching expression="palette='viridis'"/>
993 <has_text_matching expression="saturation=0.75"/>
994 </assert_contents>
995 </output>
967 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/> 996 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
968 </test> 997 </test>
969 <test> 998 <test>
970 <!-- test 6: pl.stacked_violin !--> 999 <!-- test 5: pl.stacked_violin !-->
971 <param name="adata" value="krumsiek11.h5ad" /> 1000 <param name="adata" value="krumsiek11.h5ad" />
972 <param name="format" value="png"/> 1001 <param name="format" value="png"/>
973 <conditional name="method"> 1002 <conditional name="method">
974 <param name="method" value="pl.stacked_violin"/> 1003 <param name="method" value="pl.stacked_violin"/>
975 <conditional name="var_names"> 1004 <conditional name="var_names">
1000 <param name="color" value="AliceBlue"/> 1029 <param name="color" value="AliceBlue"/>
1001 <param name="palette" value="viridis"/> 1030 <param name="palette" value="viridis"/>
1002 <param name="saturation" value="0.75"/> 1031 <param name="saturation" value="0.75"/>
1003 </section> 1032 </section>
1004 </conditional> 1033 </conditional>
1005 <assert_stdout> 1034 <section name="advanced_common">
1006 <has_text_matching expression="sc.pl.stacked_violin"/> 1035 <param name="show_log" value="true" />
1007 <has_text_matching expression="groupby='cell_type'"/> 1036 </section>
1008 <has_text_matching expression="log=False"/> 1037 <output name="hidden_output">
1009 <has_text_matching expression="use_raw=False"/> 1038 <assert_contents>
1010 <has_text_matching expression="num_categories=7"/> 1039 <has_text_matching expression="sc.pl.stacked_violin"/>
1011 <has_text_matching expression="dendrogram=True"/> 1040 <has_text_matching expression="groupby='cell_type'"/>
1012 <has_text_matching expression="swap_axes=True"/> 1041 <has_text_matching expression="log=False"/>
1013 <has_text_matching expression="stripplot=True"/> 1042 <has_text_matching expression="use_raw=False"/>
1014 <has_text_matching expression="jitter=True"/> 1043 <has_text_matching expression="num_categories=7"/>
1015 <has_text_matching expression="size=1"/> 1044 <has_text_matching expression="dendrogram=True"/>
1016 <has_text_matching expression="scale='width'"/> 1045 <has_text_matching expression="swap_axes=True"/>
1017 <has_text_matching expression="bw='scott'"/> 1046 <has_text_matching expression="stripplot=True"/>
1018 <has_text_matching expression="scale='width'"/> 1047 <has_text_matching expression="jitter=True"/>
1019 <has_text_matching expression="linewidth=0.0"/> 1048 <has_text_matching expression="size=1"/>
1020 <has_text_matching expression="color='AliceBlue'"/> 1049 <has_text_matching expression="scale='width'"/>
1021 <has_text_matching expression="palette='viridis'"/> 1050 <has_text_matching expression="bw='scott'"/>
1022 <has_text_matching expression="saturation=0.75"/> 1051 <has_text_matching expression="scale='width'"/>
1023 </assert_stdout> 1052 <has_text_matching expression="linewidth=0.0"/>
1053 <has_text_matching expression="color='AliceBlue'"/>
1054 <has_text_matching expression="palette='viridis'"/>
1055 <has_text_matching expression="saturation=0.75"/>
1056 </assert_contents>
1057 </output>
1024 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/> 1058 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
1025 </test> 1059 </test>
1026 <test> 1060 <test>
1027 <!-- test 7: pl.matrixplot !--> 1061 <!-- test 6: pl.matrixplot !-->
1028 <param name="adata" value="krumsiek11.h5ad" /> 1062 <param name="adata" value="krumsiek11.h5ad" />
1029 <param name="format" value="png"/> 1063 <param name="format" value="png"/>
1030 <conditional name="method"> 1064 <conditional name="method">
1031 <param name="method" value="pl.matrixplot"/> 1065 <param name="method" value="pl.matrixplot"/>
1032 <conditional name="var_names"> 1066 <conditional name="var_names">
1045 <param name="cmap" value="viridis"/> 1079 <param name="cmap" value="viridis"/>
1046 <param name="edgecolors" value="face"/> 1080 <param name="edgecolors" value="face"/>
1047 <param name="snap" value="False"/> 1081 <param name="snap" value="False"/>
1048 </section> 1082 </section>
1049 </conditional> 1083 </conditional>
1050 <assert_stdout> 1084 <section name="advanced_common">
1051 <has_text_matching expression="sc.pl.matrixplot"/> 1085 <param name="show_log" value="true" />
1052 <has_text_matching expression="var_names=adata.var_names" /> 1086 </section>
1053 <has_text_matching expression="groupby='cell_type'"/> 1087 <output name="hidden_output">
1054 <has_text_matching expression="log=False"/> 1088 <assert_contents>
1055 <has_text_matching expression="use_raw=False"/> 1089 <has_text_matching expression="sc.pl.matrixplot"/>
1056 <has_text_matching expression="num_categories=7"/> 1090 <has_text_matching expression="var_names=adata.var_names" />
1057 <has_text_matching expression="dendrogram=True"/> 1091 <has_text_matching expression="groupby='cell_type'"/>
1058 <has_text_matching expression="swap_axes=True"/> 1092 <has_text_matching expression="log=False"/>
1059 <has_text_matching expression="cmap='viridis'"/> 1093 <has_text_matching expression="use_raw=False"/>
1060 <has_text_matching expression="edgecolors='face'"/> 1094 <has_text_matching expression="num_categories=7"/>
1061 <has_text_matching expression="snap=False"/> 1095 <has_text_matching expression="dendrogram=True"/>
1062 </assert_stdout> 1096 <has_text_matching expression="swap_axes=True"/>
1097 <has_text_matching expression="cmap='viridis'"/>
1098 <has_text_matching expression="edgecolors='face'"/>
1099 <has_text_matching expression="snap=False"/>
1100 </assert_contents>
1101 </output>
1063 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1102 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
1064 </test> 1103 </test>
1065 <test> 1104 <test>
1066 <!-- test 8: pl.clustermap !--> 1105 <!-- test 7: pl.clustermap !-->
1067 <param name="adata" value="krumsiek11.h5ad" /> 1106 <param name="adata" value="krumsiek11.h5ad" />
1068 <param name="format" value="png"/> 1107 <param name="format" value="png"/>
1069 <conditional name="method"> 1108 <conditional name="method">
1070 <param name="method" value="pl.clustermap"/> 1109 <param name="method" value="pl.clustermap"/>
1071 <param name="use_raw" value="False"/> 1110 <param name="use_raw" value="False"/>
1076 <param name="standard_scale" value="None"/> 1115 <param name="standard_scale" value="None"/>
1077 <param name="col_cluster" value="False"/> 1116 <param name="col_cluster" value="False"/>
1078 <param name="row_cluster" value="False"/> 1117 <param name="row_cluster" value="False"/>
1079 </section> 1118 </section>
1080 </conditional> 1119 </conditional>
1081 <assert_stdout> 1120 <section name="advanced_common">
1082 <has_text_matching expression="sc.pl.clustermap"/> 1121 <param name="show_log" value="true" />
1083 <has_text_matching expression="adata=adata" /> 1122 </section>
1084 <has_text_matching expression="use_raw=False"/> 1123 <output name="hidden_output">
1085 <has_text_matching expression="method='single'"/> 1124 <assert_contents>
1086 <has_text_matching expression="metric='euclidean'"/> 1125 <has_text_matching expression="sc.pl.clustermap"/>
1087 <has_text_matching expression="col_cluster=False"/> 1126 <has_text_matching expression="adata=adata" />
1088 <has_text_matching expression="row_cluster=False"/> 1127 <has_text_matching expression="use_raw=False"/>
1089 </assert_stdout> 1128 <has_text_matching expression="method='single'"/>
1129 <has_text_matching expression="metric='euclidean'"/>
1130 <has_text_matching expression="col_cluster=False"/>
1131 <has_text_matching expression="row_cluster=False"/>
1132 </assert_contents>
1133 </output>
1090 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/> 1134 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
1091 </test> 1135 </test>
1092 <test> 1136 <test>
1093 <!-- test 9: pl.highest_expr_genes !--> 1137 <!-- test 8: pl.highest_expr_genes !-->
1094 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" /> 1138 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1095 <param name="format" value="png"/> 1139 <param name="format" value="png"/>
1096 <conditional name="method"> 1140 <conditional name="method">
1097 <param name="method" value="pl.highest_expr_genes"/> 1141 <param name="method" value="pl.highest_expr_genes"/>
1098 <param name="n_top" value="30"/> 1142 <param name="n_top" value="30"/>
1100 <section name="setseaborn_boxplot"> 1144 <section name="setseaborn_boxplot">
1101 <param name="color" value="blue"/> 1145 <param name="color" value="blue"/>
1102 <param name="saturation" value="0.5"/> 1146 <param name="saturation" value="0.5"/>
1103 </section> 1147 </section>
1104 </conditional> 1148 </conditional>
1105 <assert_stdout> 1149 <section name="advanced_common">
1106 <has_text_matching expression="sc.pl.highest_expr_genes"/> 1150 <param name="show_log" value="true" />
1107 <has_text_matching expression="n_top=30" /> 1151 </section>
1108 <has_text_matching expression="gene_symbols='means'" /> 1152 <output name="hidden_output">
1109 <has_text_matching expression="color='blue'"/> 1153 <assert_contents>
1110 <has_text_matching expression="saturation=0.5"/> 1154 <has_text_matching expression="sc.pl.highest_expr_genes"/>
1111 </assert_stdout> 1155 <has_text_matching expression="n_top=30" />
1156 <has_text_matching expression="gene_symbols='means'" />
1157 <has_text_matching expression="color='blue'"/>
1158 <has_text_matching expression="saturation=0.5"/>
1159 </assert_contents>
1160 </output>
1112 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/> 1161 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
1113 </test> 1162 </test>
1114 <test> 1163 <test>
1115 <!-- test 10: pl.highly_variable_genes !--> 1164 <!-- test 9: pl.highly_variable_genes !-->
1116 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" /> 1165 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
1117 <param name="format" value="png"/> 1166 <param name="format" value="png"/>
1118 <conditional name="method"> 1167 <conditional name="method">
1119 <param name="method" value="pl.highly_variable_genes"/> 1168 <param name="method" value="pl.highly_variable_genes"/>
1120 <param name="log" value="false"/> 1169 <param name="log" value="false"/>
1121 <param name="highly_variable_genes" value="true"/> 1170 <param name="highly_variable_genes" value="true"/>
1122 </conditional> 1171 </conditional>
1123 <assert_stdout> 1172 <section name="advanced_common">
1124 <has_text_matching expression="sc.pl.highly_variable_genes"/> 1173 <param name="show_log" value="true" />
1125 <has_text_matching expression="adata_or_result=adata" /> 1174 </section>
1126 <has_text_matching expression="log=False" /> 1175 <output name="hidden_output">
1127 <has_text_matching expression="highly_variable_genes=True"/> 1176 <assert_contents>
1128 </assert_stdout> 1177 <has_text_matching expression="sc.pl.highly_variable_genes"/>
1178 <has_text_matching expression="adata_or_result=adata" />
1179 <has_text_matching expression="log=False" />
1180 <has_text_matching expression="highly_variable_genes=True"/>
1181 </assert_contents>
1182 </output>
1129 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/> 1183 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
1130 </test> 1184 </test>
1131 <test> 1185 <test>
1132 <!-- test 11: pl.pca !--> 1186 <!-- test 10: pl.pca !-->
1133 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1187 <param name="adata" value="pbmc68k_reduced.h5ad" />
1134 <param name="format" value="pdf"/> 1188 <param name="format" value="pdf"/>
1135 <conditional name="method"> 1189 <conditional name="method">
1136 <param name="method" value="pl.pca"/> 1190 <param name="method" value="pl.pca"/>
1137 <param name="color" value="CD3D,CD79A"/> 1191 <param name="color" value="CD3D,CD79A"/>
1160 <section name="matplotlib_pyplot_scatter"> 1214 <section name="matplotlib_pyplot_scatter">
1161 <param name="linewidths" value="0"/> 1215 <param name="linewidths" value="0"/>
1162 <param name="edgecolors" value="face"/> 1216 <param name="edgecolors" value="face"/>
1163 </section> 1217 </section>
1164 </conditional> 1218 </conditional>
1165 <assert_stdout> 1219 <section name="advanced_common">
1166 <has_text_matching expression="sc.pl.pca"/> 1220 <param name="show_log" value="true" />
1167 <has_text_matching expression="save='.pdf'" /> 1221 </section>
1168 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" /> 1222 <output name="hidden_output">
1169 <has_text_matching expression="use_raw=False" /> 1223 <assert_contents>
1170 <has_text_matching expression="sort_order=True" /> 1224 <has_text_matching expression="sc.pl.pca"/>
1171 <has_text_matching expression="components=\['1,2', '1,3'\]" /> 1225 <has_text_matching expression="save='.pdf'" />
1172 <has_text_matching expression="projection='2d'" /> 1226 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
1173 <has_text_matching expression="legend_loc='right margin'" /> 1227 <has_text_matching expression="use_raw=False" />
1174 <has_text_matching expression="legend_fontsize=1" /> 1228 <has_text_matching expression="sort_order=True" />
1175 <has_text_matching expression="legend_fontweight='normal'" /> 1229 <has_text_matching expression="components=\['1,2', '1,3'\]" />
1176 <has_text_matching expression="size=1.0" /> 1230 <has_text_matching expression="projection='2d'" />
1177 <has_text_matching expression="palette='viridis'" /> 1231 <has_text_matching expression="legend_loc='right margin'" />
1178 <has_text_matching expression="frameon=True" /> 1232 <has_text_matching expression="legend_fontsize=1" />
1179 <has_text_matching expression="ncols=2" /> 1233 <has_text_matching expression="legend_fontweight='normal'" />
1180 <has_text_matching expression="wspace=0.1" /> 1234 <has_text_matching expression="size=1.0" />
1181 <has_text_matching expression="hspace=0.25" /> 1235 <has_text_matching expression="palette='viridis'" />
1182 <has_text_matching expression="linewidths=0.0" /> 1236 <has_text_matching expression="frameon=True" />
1183 <has_text_matching expression="edgecolors='face" /> 1237 <has_text_matching expression="ncols=2" />
1184 </assert_stdout> 1238 <has_text_matching expression="wspace=0.1" />
1239 <has_text_matching expression="hspace=0.25" />
1240 <has_text_matching expression="linewidths=0.0" />
1241 <has_text_matching expression="edgecolors='face" />
1242 </assert_contents>
1243 </output>
1185 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> 1244 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
1186 </test> 1245 </test>
1187 <test> 1246 <test>
1188 <!-- test 12: pl.pca_loadings !--> 1247 <!-- test 11: pl.pca_loadings !-->
1189 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1248 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1190 <param name="format" value="png"/> 1249 <param name="format" value="png"/>
1191 <conditional name="method"> 1250 <conditional name="method">
1192 <param name="method" value="pl.pca_loadings"/> 1251 <param name="method" value="pl.pca_loadings"/>
1193 <param name="components" value="1,2,3"/> 1252 <param name="components" value="1,2,3"/>
1194 </conditional> 1253 </conditional>
1195 <assert_stdout> 1254 <section name="advanced_common">
1196 <has_text_matching expression="sc.pl.pca_loadings"/> 1255 <param name="show_log" value="true" />
1197 <has_text_matching expression="components=\[1, 2, 3\]" /> 1256 </section>
1198 </assert_stdout> 1257 <output name="hidden_output">
1258 <assert_contents>
1259 <has_text_matching expression="sc.pl.pca_loadings"/>
1260 <has_text_matching expression="components=\[1, 2, 3\]" />
1261 </assert_contents>
1262 </output>
1199 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/> 1263 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
1200 </test> 1264 </test>
1201 <test> 1265 <test>
1202 <!-- test 13: pl.pca_variance_ratio !--> 1266 <!-- test 12: pl.pca_variance_ratio !-->
1203 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1267 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1204 <param name="format" value="png"/> 1268 <param name="format" value="png"/>
1205 <conditional name="method"> 1269 <conditional name="method">
1206 <param name="method" value="pl.pca_variance_ratio"/> 1270 <param name="method" value="pl.pca_variance_ratio"/>
1207 <param name="n_pcs" value="5"/> 1271 <param name="n_pcs" value="5"/>
1208 <param name="log" value="False"/> 1272 <param name="log" value="False"/>
1209 </conditional> 1273 </conditional>
1210 <assert_stdout> 1274 <section name="advanced_common">
1211 <has_text_matching expression="sc.pl.pca_variance_ratio"/> 1275 <param name="show_log" value="true" />
1212 <has_text_matching expression="n_pcs=5" /> 1276 </section>
1213 <has_text_matching expression="log=False" /> 1277 <output name="hidden_output">
1214 </assert_stdout> 1278 <assert_contents>
1279 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
1280 <has_text_matching expression="n_pcs=5" />
1281 <has_text_matching expression="log=False" />
1282 </assert_contents>
1283 </output>
1215 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/> 1284 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
1216 </test> 1285 </test>
1217 <test> 1286 <test>
1218 <!-- test 14: pl.pca_overview !--> 1287 <!-- test 13: pl.pca_overview !-->
1219 <param name="adata" value="pp.pca.krumsiek11.h5ad" /> 1288 <param name="adata" value="pp.pca.krumsiek11.h5ad" />
1220 <param name="format" value="png"/> 1289 <param name="format" value="png"/>
1221 <conditional name="method"> 1290 <conditional name="method">
1222 <param name="method" value="pl.pca_overview"/> 1291 <param name="method" value="pl.pca_overview"/>
1223 <param name="use_raw" value="False"/> 1292 <param name="use_raw" value="False"/>
1233 <param name="ncols" value="4"/> 1302 <param name="ncols" value="4"/>
1234 <param name="wspace" value="0.1"/> 1303 <param name="wspace" value="0.1"/>
1235 <param name="hspace" value="0.25"/> 1304 <param name="hspace" value="0.25"/>
1236 </section> 1305 </section>
1237 </conditional> 1306 </conditional>
1238 <assert_stdout> 1307 <section name="advanced_common">
1239 <has_text_matching expression="sc.pl.pca_overview"/> 1308 <param name="show_log" value="true" />
1240 <has_text_matching expression="use_raw=False"/> 1309 </section>
1241 <has_text_matching expression="sort_order=True"/> 1310 <output name="hidden_output">
1242 <has_text_matching expression="projection='2d'"/> 1311 <assert_contents>
1243 <has_text_matching expression="legend_loc='right margin'"/> 1312 <has_text_matching expression="sc.pl.pca_overview"/>
1244 <has_text_matching expression="legend_fontsize=1"/> 1313 <has_text_matching expression="use_raw=False"/>
1245 <has_text_matching expression="legend_fontweight='normal'"/> 1314 <has_text_matching expression="sort_order=True"/>
1246 <has_text_matching expression="size=1.0"/> 1315 <has_text_matching expression="projection='2d'"/>
1247 <has_text_matching expression="palette='viridis'"/> 1316 <has_text_matching expression="legend_loc='right margin'"/>
1248 <has_text_matching expression="frameon=True"/> 1317 <has_text_matching expression="legend_fontsize=1"/>
1249 <has_text_matching expression="ncols=4"/> 1318 <has_text_matching expression="legend_fontweight='normal'"/>
1250 <has_text_matching expression="wspace=0.1"/> 1319 <has_text_matching expression="size=1.0"/>
1251 <has_text_matching expression="hspace=0.25"/> 1320 <has_text_matching expression="palette='viridis'"/>
1252 </assert_stdout> 1321 <has_text_matching expression="frameon=True"/>
1322 <has_text_matching expression="ncols=4"/>
1323 <has_text_matching expression="wspace=0.1"/>
1324 <has_text_matching expression="hspace=0.25"/>
1325 </assert_contents>
1326 </output>
1253 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/> 1327 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
1254 </test> 1328 </test>
1255 <test> 1329 <test>
1256 <!-- test 15: pl.tsne !--> 1330 <!-- test 14: pl.tsne !-->
1257 <param name="adata" value="tl.tsne.krumsiek11.h5ad" /> 1331 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />
1258 <param name="format" value="png"/> 1332 <param name="format" value="png"/>
1259 <conditional name="method"> 1333 <conditional name="method">
1260 <param name="method" value="pl.tsne"/> 1334 <param name="method" value="pl.tsne"/>
1261 <param name="use_raw" value="False"/> 1335 <param name="use_raw" value="False"/>
1279 <section name="matplotlib_pyplot_scatter"> 1353 <section name="matplotlib_pyplot_scatter">
1280 <param name="linewidths" value="0"/> 1354 <param name="linewidths" value="0"/>
1281 <param name="edgecolors" value="face"/> 1355 <param name="edgecolors" value="face"/>
1282 </section> 1356 </section>
1283 </conditional> 1357 </conditional>
1284 <assert_stdout> 1358 <section name="advanced_common">
1285 <has_text_matching expression="sc.pl.tsne"/> 1359 <param name="show_log" value="true" />
1286 <has_text_matching expression="use_raw=False"/> 1360 </section>
1287 <has_text_matching expression="edges=False"/> 1361 <output name="hidden_output">
1288 <has_text_matching expression="arrows=False"/> 1362 <assert_contents>
1289 <has_text_matching expression="sort_order=True"/> 1363 <has_text_matching expression="sc.pl.tsne"/>
1290 <has_text_matching expression="projection='2d'"/> 1364 <has_text_matching expression="use_raw=False"/>
1291 <has_text_matching expression="legend_loc='right margin'"/> 1365 <has_text_matching expression="edges=False"/>
1292 <has_text_matching expression="legend_fontsize=1"/> 1366 <has_text_matching expression="arrows=False"/>
1293 <has_text_matching expression="legend_fontweight='normal'"/> 1367 <has_text_matching expression="sort_order=True"/>
1294 <has_text_matching expression="size=1.0"/> 1368 <has_text_matching expression="projection='2d'"/>
1295 <has_text_matching expression="palette='viridis'"/> 1369 <has_text_matching expression="legend_loc='right margin'"/>
1296 <has_text_matching expression="frameon=True"/> 1370 <has_text_matching expression="legend_fontsize=1"/>
1297 <has_text_matching expression="ncols=4"/> 1371 <has_text_matching expression="legend_fontweight='normal'"/>
1298 <has_text_matching expression="wspace=0.1"/> 1372 <has_text_matching expression="size=1.0"/>
1299 <has_text_matching expression="hspace=0.25"/> 1373 <has_text_matching expression="palette='viridis'"/>
1300 <has_text_matching expression="linewidths=0.0"/> 1374 <has_text_matching expression="frameon=True"/>
1301 <has_text_matching expression="edgecolors='face'"/> 1375 <has_text_matching expression="ncols=4"/>
1302 </assert_stdout> 1376 <has_text_matching expression="wspace=0.1"/>
1377 <has_text_matching expression="hspace=0.25"/>
1378 <has_text_matching expression="linewidths=0.0"/>
1379 <has_text_matching expression="edgecolors='face'"/>
1380 </assert_contents>
1381 </output>
1303 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/> 1382 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
1304 </test> 1383 </test>
1305 <test> 1384 <test>
1306 <!-- test 16: pl.umap !--> 1385 <!-- test 15: pl.umap !-->
1307 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 1386 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1308 <param name="format" value="png"/> 1387 <param name="format" value="png"/>
1309 <conditional name="method"> 1388 <conditional name="method">
1310 <param name="method" value="pl.umap"/> 1389 <param name="method" value="pl.umap"/>
1311 <param name="color" value="paul15_clusters"/> 1390 <param name="color" value="paul15_clusters"/>
1331 <section name="matplotlib_pyplot_scatter"> 1410 <section name="matplotlib_pyplot_scatter">
1332 <param name="linewidths" value="0"/> 1411 <param name="linewidths" value="0"/>
1333 <param name="edgecolors" value="face"/> 1412 <param name="edgecolors" value="face"/>
1334 </section> 1413 </section>
1335 </conditional> 1414 </conditional>
1336 <assert_stdout> 1415 <section name="advanced_common">
1337 <has_text_matching expression="sc.pl.umap"/> 1416 <param name="show_log" value="true" />
1338 <has_text_matching expression="color=\['paul15_clusters'\]"/> 1417 </section>
1339 <has_text_matching expression="use_raw=False"/> 1418 <output name="hidden_output">
1340 <has_text_matching expression="edges=True"/> 1419 <assert_contents>
1341 <has_text_matching expression="edges_width=0.1"/> 1420 <has_text_matching expression="sc.pl.umap"/>
1342 <has_text_matching expression="edges_color='AliceBlue'"/> 1421 <has_text_matching expression="color=\['paul15_clusters'\]"/>
1343 <has_text_matching expression="arrows=False"/> 1422 <has_text_matching expression="use_raw=False"/>
1344 <has_text_matching expression="sort_order=True"/> 1423 <has_text_matching expression="edges=True"/>
1345 <has_text_matching expression="projection='2d'"/> 1424 <has_text_matching expression="edges_width=0.1"/>
1346 <has_text_matching expression="legend_loc='right margin'"/> 1425 <has_text_matching expression="edges_color='AliceBlue'"/>
1347 <has_text_matching expression="legend_fontsize=1"/> 1426 <has_text_matching expression="arrows=False"/>
1348 <has_text_matching expression="legend_fontweight='normal'"/> 1427 <has_text_matching expression="sort_order=True"/>
1349 <has_text_matching expression="size=1.0"/> 1428 <has_text_matching expression="projection='2d'"/>
1350 <has_text_matching expression="palette='viridis'"/> 1429 <has_text_matching expression="legend_loc='right margin'"/>
1351 <has_text_matching expression="frameon=True"/> 1430 <has_text_matching expression="legend_fontsize=1"/>
1352 <has_text_matching expression="ncols=4"/> 1431 <has_text_matching expression="legend_fontweight='normal'"/>
1353 <has_text_matching expression="wspace=0.1"/> 1432 <has_text_matching expression="size=1.0"/>
1354 <has_text_matching expression="hspace=0.25"/> 1433 <has_text_matching expression="palette='viridis'"/>
1355 <has_text_matching expression="linewidths=0.0"/> 1434 <has_text_matching expression="frameon=True"/>
1356 <has_text_matching expression="edgecolors='face'"/> 1435 <has_text_matching expression="ncols=4"/>
1357 </assert_stdout> 1436 <has_text_matching expression="wspace=0.1"/>
1437 <has_text_matching expression="hspace=0.25"/>
1438 <has_text_matching expression="linewidths=0.0"/>
1439 <has_text_matching expression="edgecolors='face'"/>
1440 </assert_contents>
1441 </output>
1358 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1442 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1359 </test> 1443 </test>
1360 <test> 1444 <test>
1361 <!-- test 17: pl.diffmap !--> 1445 <!-- test 16: pl.diffmap !-->
1362 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1446 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1363 <param name="format" value="png"/> 1447 <param name="format" value="png"/>
1364 <conditional name="method"> 1448 <conditional name="method">
1365 <param name="method" value="pl.diffmap"/> 1449 <param name="method" value="pl.diffmap"/>
1366 <param name="color" value="paul15_clusters"/> 1450 <param name="color" value="paul15_clusters"/>
1381 <section name="matplotlib_pyplot_scatter"> 1465 <section name="matplotlib_pyplot_scatter">
1382 <param name="linewidths" value="0"/> 1466 <param name="linewidths" value="0"/>
1383 <param name="edgecolors" value="face"/> 1467 <param name="edgecolors" value="face"/>
1384 </section> 1468 </section>
1385 </conditional> 1469 </conditional>
1386 <assert_stdout> 1470 <section name="advanced_common">
1387 <has_text_matching expression="sc.pl.diffmap"/> 1471 <param name="show_log" value="true" />
1388 <has_text_matching expression="color=\['paul15_clusters'\]"/> 1472 </section>
1389 <has_text_matching expression="use_raw=False"/> 1473 <output name="hidden_output">
1390 <has_text_matching expression="sort_order=True"/> 1474 <assert_contents>
1391 <has_text_matching expression="projection='2d'"/> 1475 <has_text_matching expression="sc.pl.diffmap"/>
1392 <has_text_matching expression="legend_loc='right margin'"/> 1476 <has_text_matching expression="color=\['paul15_clusters'\]"/>
1393 <has_text_matching expression="legend_fontsize=1"/> 1477 <has_text_matching expression="use_raw=False"/>
1394 <has_text_matching expression="legend_fontweight='normal'"/> 1478 <has_text_matching expression="sort_order=True"/>
1395 <has_text_matching expression="size=1.0"/> 1479 <has_text_matching expression="projection='2d'"/>
1396 <has_text_matching expression="palette='viridis'"/> 1480 <has_text_matching expression="legend_loc='right margin'"/>
1397 <has_text_matching expression="frameon=True"/> 1481 <has_text_matching expression="legend_fontsize=1"/>
1398 <has_text_matching expression="ncols=4"/> 1482 <has_text_matching expression="legend_fontweight='normal'"/>
1399 <has_text_matching expression="wspace=0.1"/> 1483 <has_text_matching expression="size=1.0"/>
1400 <has_text_matching expression="hspace=0.25"/> 1484 <has_text_matching expression="palette='viridis'"/>
1401 <has_text_matching expression="linewidths=0.0"/> 1485 <has_text_matching expression="frameon=True"/>
1402 <has_text_matching expression="edgecolors='face'"/> 1486 <has_text_matching expression="ncols=4"/>
1403 </assert_stdout> 1487 <has_text_matching expression="wspace=0.1"/>
1488 <has_text_matching expression="hspace=0.25"/>
1489 <has_text_matching expression="linewidths=0.0"/>
1490 <has_text_matching expression="edgecolors='face'"/>
1491 </assert_contents>
1492 </output>
1404 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1493 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1405 </test> 1494 </test>
1406 <test> 1495 <test>
1407 <!-- test 18: pl.draw_graph !--> 1496 <!-- test 17: pl.draw_graph !-->
1408 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 1497 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1409 <param name="format" value="png"/> 1498 <param name="format" value="png"/>
1410 <conditional name="method"> 1499 <conditional name="method">
1411 <param name="method" value="pl.draw_graph"/> 1500 <param name="method" value="pl.draw_graph"/>
1412 <param name="use_raw" value="false"/> 1501 <param name="use_raw" value="false"/>
1430 <section name="matplotlib_pyplot_scatter"> 1519 <section name="matplotlib_pyplot_scatter">
1431 <param name="linewidths" value="0"/> 1520 <param name="linewidths" value="0"/>
1432 <param name="edgecolors" value="face"/> 1521 <param name="edgecolors" value="face"/>
1433 </section> 1522 </section>
1434 </conditional> 1523 </conditional>
1435 <assert_stdout> 1524 <section name="advanced_common">
1436 <has_text_matching expression="sc.pl.draw_graph"/> 1525 <param name="show_log" value="true" />
1437 <has_text_matching expression="use_raw=False"/> 1526 </section>
1438 <has_text_matching expression="edges=True"/> 1527 <output name="hidden_output">
1439 <has_text_matching expression="edges_width=0.1"/> 1528 <assert_contents>
1440 <has_text_matching expression="edges_color='Crimson'"/> 1529 <has_text_matching expression="sc.pl.draw_graph"/>
1441 <has_text_matching expression="arrows=False"/> 1530 <has_text_matching expression="use_raw=False"/>
1442 <has_text_matching expression="sort_order=False"/> 1531 <has_text_matching expression="edges=True"/>
1443 <has_text_matching expression="projection='2d'"/> 1532 <has_text_matching expression="edges_width=0.1"/>
1444 <has_text_matching expression="legend_loc='right margin'"/> 1533 <has_text_matching expression="edges_color='Crimson'"/>
1445 <has_text_matching expression="legend_fontweight='normal'"/> 1534 <has_text_matching expression="arrows=False"/>
1446 <has_text_matching expression="palette='viridis'"/> 1535 <has_text_matching expression="sort_order=False"/>
1447 <has_text_matching expression="frameon=True"/> 1536 <has_text_matching expression="projection='2d'"/>
1448 <has_text_matching expression="ncols=4"/> 1537 <has_text_matching expression="legend_loc='right margin'"/>
1449 <has_text_matching expression="wspace=0.1"/> 1538 <has_text_matching expression="legend_fontweight='normal'"/>
1450 <has_text_matching expression="hspace=0.25"/> 1539 <has_text_matching expression="palette='viridis'"/>
1451 <has_text_matching expression="linewidths=0.0"/> 1540 <has_text_matching expression="frameon=True"/>
1452 <has_text_matching expression="edgecolors='face"/> 1541 <has_text_matching expression="ncols=4"/>
1453 </assert_stdout> 1542 <has_text_matching expression="wspace=0.1"/>
1543 <has_text_matching expression="hspace=0.25"/>
1544 <has_text_matching expression="linewidths=0.0"/>
1545 <has_text_matching expression="edgecolors='face"/>
1546 </assert_contents>
1547 </output>
1454 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/> 1548 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
1455 </test> 1549 </test>
1456 <!--<test> 1550 <!--<test>
1457 < test pl.dpt_groups_pseudotime > 1551 < test pl.dpt_groups_pseudotime >
1458 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1552 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1466 <has_text_matching expression="color_map='viridis'"/> 1560 <has_text_matching expression="color_map='viridis'"/>
1467 </assert_stdout> 1561 </assert_stdout>
1468 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1562 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1469 </test>!--> 1563 </test>!-->
1470 <test> 1564 <test>
1471 <!-- test 19: pl.dpt_timeseries !--> 1565 <!-- test 18: pl.dpt_timeseries !-->
1472 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 1566 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
1473 <param name="format" value="png"/> 1567 <param name="format" value="png"/>
1474 <conditional name="method"> 1568 <conditional name="method">
1475 <param name="method" value="pl.dpt_timeseries"/> 1569 <param name="method" value="pl.dpt_timeseries"/>
1476 <conditional name="heatmap"> 1570 <conditional name="heatmap">
1477 <param name="as_heatmap" value="True"/> 1571 <param name="as_heatmap" value="True"/>
1478 <param name="color_map" value="viridis"/> 1572 <param name="color_map" value="viridis"/>
1479 </conditional> 1573 </conditional>
1480 </conditional> 1574 </conditional>
1481 <assert_stdout> 1575 <section name="advanced_common">
1482 <has_text_matching expression="sc.pl.dpt_timeseries"/> 1576 <param name="show_log" value="true" />
1483 <has_text_matching expression="color_map='viridis'"/> 1577 </section>
1484 <has_text_matching expression="as_heatmap=True"/> 1578 <output name="hidden_output">
1485 </assert_stdout> 1579 <assert_contents>
1580 <has_text_matching expression="sc.pl.dpt_timeseries"/>
1581 <has_text_matching expression="color_map='viridis'"/>
1582 <has_text_matching expression="as_heatmap=True"/>
1583 </assert_contents>
1584 </output>
1486 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/> 1585 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
1487 </test> 1586 </test>
1488 <!--<test> 1587 <!--<test>
1489 test pl.paga 1588 test pl.paga
1490 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" /> 1589 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
1512 <!--<test> 1611 <!--<test>
1513 test pl.paga_compare 1612 test pl.paga_compare
1514 </test>!--> 1613 </test>!-->
1515 <!--<test> 1614 <!--<test>
1516 test pl.paga_path 1615 test pl.paga_path
1517 </test>!--> 1616 </test>!-->
1518 <test> 1617 <test>
1519 <!-- test 20: pl.rank_genes_groups !--> 1618 <!-- test 19: pl.rank_genes_groups !-->
1520 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1619 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1521 <param name="format" value="png"/> 1620 <param name="format" value="png"/>
1522 <conditional name="method"> 1621 <conditional name="method">
1523 <param name="method" value="pl.rank_genes_groups"/> 1622 <param name="method" value="pl.rank_genes_groups"/>
1524 <param name="n_genes" value="10"/> 1623 <param name="n_genes" value="10"/>
1525 <param name="fontsize" value="8"/> 1624 <param name="fontsize" value="8"/>
1526 <param name="ncols" value="4"/> 1625 <param name="ncols" value="4"/>
1527 <param name="sharey" value="true"/> 1626 <param name="sharey" value="true"/>
1528 </conditional> 1627 </conditional>
1529 <assert_stdout> 1628 <section name="advanced_common">
1530 <has_text_matching expression="sc.pl.rank_genes_groups"/> 1629 <param name="show_log" value="true" />
1531 <has_text_matching expression="n_genes=10"/> 1630 </section>
1532 <has_text_matching expression="fontsize=8"/> 1631 <output name="hidden_output">
1533 <has_text_matching expression="ncols=4"/> 1632 <assert_contents>
1534 <has_text_matching expression="sharey=True"/> 1633 <has_text_matching expression="sc.pl.rank_genes_groups"/>
1535 </assert_stdout> 1634 <has_text_matching expression="n_genes=10"/>
1635 <has_text_matching expression="fontsize=8"/>
1636 <has_text_matching expression="ncols=4"/>
1637 <has_text_matching expression="sharey=True"/>
1638 </assert_contents>
1639 </output>
1536 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1640 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1537 </test> 1641 </test>
1538 <test> 1642 <test>
1539 <!-- test 21: pl.rank_genes_groups_violin !--> 1643 <!-- test 20: pl.rank_genes_groups_violin !-->
1540 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1644 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1541 <param name="format" value="png"/> 1645 <param name="format" value="png"/>
1542 <conditional name="method"> 1646 <conditional name="method">
1543 <param name="method" value="pl.rank_genes_groups_violin"/> 1647 <param name="method" value="pl.rank_genes_groups_violin"/>
1544 <conditional name="genes"> 1648 <conditional name="genes">
1554 <param name="size" value="1"/> 1658 <param name="size" value="1"/>
1555 </conditional> 1659 </conditional>
1556 <param name="scale" value="width"/> 1660 <param name="scale" value="width"/>
1557 </section> 1661 </section>
1558 </conditional> 1662 </conditional>
1559 <assert_stdout> 1663 <section name="advanced_common">
1560 <has_text_matching expression="sc.pl.rank_genes_groups_violin"/> 1664 <param name="show_log" value="true" />
1561 <has_text_matching expression="n_genes=10"/> 1665 </section>
1562 <has_text_matching expression="use_raw=False"/> 1666 <output name="hidden_output">
1563 <has_text_matching expression="split=True"/> 1667 <assert_contents>
1564 <has_text_matching expression="strip=True"/> 1668 <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
1565 <has_text_matching expression="jitter=True"/> 1669 <has_text_matching expression="n_genes=10"/>
1566 <has_text_matching expression="size=1"/> 1670 <has_text_matching expression="use_raw=False"/>
1567 <has_text_matching expression="scale='width'"/> 1671 <has_text_matching expression="split=True"/>
1568 </assert_stdout> 1672 <has_text_matching expression="strip=True"/>
1673 <has_text_matching expression="jitter=True"/>
1674 <has_text_matching expression="size=1"/>
1675 <has_text_matching expression="scale='width'"/>
1676 </assert_contents>
1677 </output>
1569 <output_collection name="collection_png"> 1678 <output_collection name="collection_png">
1570 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/> 1679 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
1571 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/> 1680 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
1572 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> 1681 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
1573 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> 1682 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
1574 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> 1683 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1575 </output_collection> 1684 </output_collection>
1576 </test> 1685 </test>
1577 <test> 1686 <test>
1578 <!-- test 22: pl.rank_genes_groups_dotplot !--> 1687 <!-- test 21: pl.rank_genes_groups_dotplot !-->
1579 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1688 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1580 <param name="format" value="png"/> 1689 <param name="format" value="png"/>
1581 <conditional name="method"> 1690 <conditional name="method">
1582 <param name="method" value="pl.rank_genes_groups_dotplot"/> 1691 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1583 <param name="n_genes" value="10"/> 1692 <param name="n_genes" value="10"/>
1588 <section name="matplotlib_pyplot_scatter"> 1697 <section name="matplotlib_pyplot_scatter">
1589 <param name="linewidths" value="0" /> 1698 <param name="linewidths" value="0" />
1590 <param name="edgecolors" value="face"/> 1699 <param name="edgecolors" value="face"/>
1591 </section> 1700 </section>
1592 </conditional> 1701 </conditional>
1593 <assert_stdout> 1702 <section name="advanced_common">
1594 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/> 1703 <param name="show_log" value="true" />
1595 <has_text_matching expression="n_genes=10"/> 1704 </section>
1596 <has_text_matching expression="log=False"/> 1705 <output name="hidden_output">
1597 <has_text_matching expression="use_raw=False"/> 1706 <assert_contents>
1598 <has_text_matching expression="dendrogram=False"/> 1707 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1599 <has_text_matching expression="color_map='viridis'"/> 1708 <has_text_matching expression="n_genes=10"/>
1600 <has_text_matching expression="linewidths=0.0"/> 1709 <has_text_matching expression="log=False"/>
1601 <has_text_matching expression="edgecolors='face'"/> 1710 <has_text_matching expression="use_raw=False"/>
1602 </assert_stdout> 1711 <has_text_matching expression="dendrogram=False"/>
1712 <has_text_matching expression="color_map='viridis'"/>
1713 <has_text_matching expression="linewidths=0.0"/>
1714 <has_text_matching expression="edgecolors='face'"/>
1715 </assert_contents>
1716 </output>
1603 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1717 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1604 </test> 1718 </test>
1605 <test> 1719 <test>
1606 <!-- test 23: pl.rank_genes_groups_heatmap !--> 1720 <!-- test 22: pl.rank_genes_groups_heatmap !-->
1607 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1721 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1608 <param name="format" value="png"/> 1722 <param name="format" value="png"/>
1609 <conditional name="method"> 1723 <conditional name="method">
1610 <param name="method" value="pl.rank_genes_groups_heatmap"/> 1724 <param name="method" value="pl.rank_genes_groups_heatmap"/>
1611 <param name="n_genes" value="10"/> 1725 <param name="n_genes" value="10"/>
1618 <param name="cmap" value="viridis"/> 1732 <param name="cmap" value="viridis"/>
1619 <param name="interpolation" value="None"/> 1733 <param name="interpolation" value="None"/>
1620 <param name="origin" value="upper"/> 1734 <param name="origin" value="upper"/>
1621 </section> 1735 </section>
1622 </conditional> 1736 </conditional>
1623 <assert_stdout> 1737 <section name="advanced_common">
1624 <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/> 1738 <param name="show_log" value="true" />
1625 <has_text_matching expression="n_genes=10"/> 1739 </section>
1626 <has_text_matching expression="log=False"/> 1740 <output name="hidden_output">
1627 <has_text_matching expression="use_raw=False"/> 1741 <assert_contents>
1628 <has_text_matching expression="dendrogram=False"/> 1742 <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
1629 <has_text_matching expression="swap_axes=False"/> 1743 <has_text_matching expression="n_genes=10"/>
1630 <has_text_matching expression="show_gene_labels=False"/> 1744 <has_text_matching expression="log=False"/>
1631 <has_text_matching expression="cmap='viridis'"/> 1745 <has_text_matching expression="use_raw=False"/>
1632 <has_text_matching expression="origin='upper'"/> 1746 <has_text_matching expression="dendrogram=False"/>
1633 </assert_stdout> 1747 <has_text_matching expression="swap_axes=False"/>
1748 <has_text_matching expression="show_gene_labels=False"/>
1749 <has_text_matching expression="cmap='viridis'"/>
1750 <has_text_matching expression="origin='upper'"/>
1751 </assert_contents>
1752 </output>
1634 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1753 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1635 </test> 1754 </test>
1636 <test> 1755 <test>
1637 <!-- test 24: pl.rank_genes_groups_matrixplot !--> 1756 <!-- test 23: pl.rank_genes_groups_matrixplot !-->
1638 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1757 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1639 <param name="format" value="png"/> 1758 <param name="format" value="png"/>
1640 <conditional name="method"> 1759 <conditional name="method">
1641 <param name="method" value="pl.rank_genes_groups_matrixplot"/> 1760 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
1642 <param name="n_genes" value="10"/> 1761 <param name="n_genes" value="10"/>
1648 <param name="cmap" value="viridis"/> 1767 <param name="cmap" value="viridis"/>
1649 <param name="edgecolors" value="face"/> 1768 <param name="edgecolors" value="face"/>
1650 <param name="snap" value="False"/> 1769 <param name="snap" value="False"/>
1651 </section> 1770 </section>
1652 </conditional> 1771 </conditional>
1653 <assert_stdout> 1772 <section name="advanced_common">
1654 <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/> 1773 <param name="show_log" value="true" />
1655 <has_text_matching expression="n_genes=10"/> 1774 </section>
1656 <has_text_matching expression="log=False"/> 1775 <output name="hidden_output">
1657 <has_text_matching expression="use_raw=False"/> 1776 <assert_contents>
1658 <has_text_matching expression="dendrogram=False"/> 1777 <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
1659 <has_text_matching expression="swap_axes=False"/> 1778 <has_text_matching expression="n_genes=10"/>
1660 <has_text_matching expression="cmap='viridis'"/> 1779 <has_text_matching expression="log=False"/>
1661 <has_text_matching expression="edgecolors='face'"/> 1780 <has_text_matching expression="use_raw=False"/>
1662 <has_text_matching expression="snap=False"/> 1781 <has_text_matching expression="dendrogram=False"/>
1663 </assert_stdout> 1782 <has_text_matching expression="swap_axes=False"/>
1783 <has_text_matching expression="cmap='viridis'"/>
1784 <has_text_matching expression="edgecolors='face'"/>
1785 <has_text_matching expression="snap=False"/>
1786 </assert_contents>
1787 </output>
1664 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1788 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1665 </test> 1789 </test>
1666 <test> 1790 <test>
1667 <!-- test 25: pl.rank_genes_groups_stacked_violin !--> 1791 <!-- test 24: pl.rank_genes_groups_stacked_violin !-->
1668 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1792 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1669 <param name="format" value="png"/> 1793 <param name="format" value="png"/>
1670 <conditional name="method"> 1794 <conditional name="method">
1671 <param name="method" value="pl.rank_genes_groups_stacked_violin"/> 1795 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
1672 <param name="n_genes" value="10"/> 1796 <param name="n_genes" value="10"/>
1690 <param name="color" value="AliceBlue"/> 1814 <param name="color" value="AliceBlue"/>
1691 <param name="palette" value="viridis"/> 1815 <param name="palette" value="viridis"/>
1692 <param name="saturation" value="0.75"/> 1816 <param name="saturation" value="0.75"/>
1693 </section> 1817 </section>
1694 </conditional> 1818 </conditional>
1695 <assert_stdout> 1819 <section name="advanced_common">
1696 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/> 1820 <param name="show_log" value="true" />
1697 <has_text_matching expression="n_genes=10"/> 1821 </section>
1698 <has_text_matching expression="log=False"/> 1822 <output name="hidden_output">
1699 <has_text_matching expression="use_raw=False"/> 1823 <assert_contents>
1700 <has_text_matching expression="dendrogram=True"/> 1824 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
1701 <has_text_matching expression="swap_axes=True"/> 1825 <has_text_matching expression="n_genes=10"/>
1702 <has_text_matching expression="stripplot=True"/> 1826 <has_text_matching expression="log=False"/>
1703 <has_text_matching expression="jitter=True"/> 1827 <has_text_matching expression="use_raw=False"/>
1704 <has_text_matching expression="size=1"/> 1828 <has_text_matching expression="dendrogram=True"/>
1705 <has_text_matching expression="scale='width'"/> 1829 <has_text_matching expression="swap_axes=True"/>
1706 <has_text_matching expression="bw='scott'"/> 1830 <has_text_matching expression="stripplot=True"/>
1707 <has_text_matching expression="scale='width'"/> 1831 <has_text_matching expression="jitter=True"/>
1708 <has_text_matching expression="linewidth=0.0"/> 1832 <has_text_matching expression="size=1"/>
1709 <has_text_matching expression="color='AliceBlue'"/> 1833 <has_text_matching expression="scale='width'"/>
1710 <has_text_matching expression="palette='viridis'"/> 1834 <has_text_matching expression="bw='scott'"/>
1711 <has_text_matching expression="saturation=0.75"/> 1835 <has_text_matching expression="scale='width'"/>
1712 </assert_stdout> 1836 <has_text_matching expression="linewidth=0.0"/>
1837 <has_text_matching expression="color='AliceBlue'"/>
1838 <has_text_matching expression="palette='viridis'"/>
1839 <has_text_matching expression="saturation=0.75"/>
1840 </assert_contents>
1841 </output>
1713 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1842 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1714 </test> 1843 </test>
1715 </tests> 1844 </tests>
1716 <help><![CDATA[ 1845 <help><![CDATA[
1717 Generic: Scatter plot along observations or variables axes (`pl.scatter`) 1846 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
1761 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__ 1890 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.violin.html>`__
1762 1891
1763 Generic: Stacked violin plots (`pl.stacked_violin`) 1892 Generic: Stacked violin plots (`pl.stacked_violin`)
1764 =================================================== 1893 ===================================================
1765 1894
1766 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`) 1895 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
1767 stacked on top of each other. Useful to visualize gene expression per cluster. 1896 stacked on top of each other. Useful to visualize gene expression per cluster.
1768 1897
1769 More details on the `scanpy documentation 1898 More details on the `scanpy documentation
1770 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__ 1899 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__
1771 1900