Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 8:6adf98e782f3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
author iuc
date Tue, 16 Mar 2021 13:01:04 +0000
parents 7647e5cd1b8b
children 9a169729c9f9
comparison
equal deleted inserted replaced
7:7647e5cd1b8b 8:6adf98e782f3
43 @CMD_params_groups@ 43 @CMD_params_groups@
44 @CMD_params_pl_components@ 44 @CMD_params_pl_components@
45 projection='$method.plot.projection', 45 projection='$method.plot.projection',
46 legend_loc='$method.plot.legend_loc', 46 legend_loc='$method.plot.legend_loc',
47 #if $method.plot.palette != 'default' 47 #if $method.plot.palette != 'default'
48 palette='$method.plot.palette', 48 palette=['$method.plot.palette'],
49 #end if 49 #end if
50 #if $method.plot.color_map != 'None' 50 #if $method.plot.color_map != 'None'
51 color_map='$method.plot.color_map', 51 color_map='$method.plot.color_map',
52 #end if 52 #end if
53 @CMD_param_legend_fontsize@ 53 @CMD_param_legend_fontsize@
237 @CMD_param_color@ 237 @CMD_param_color@
238 #if str($method.gene_symbols) != '' 238 #if str($method.gene_symbols) != ''
239 gene_symbols='$method.gene_symbols', 239 gene_symbols='$method.gene_symbols',
240 #end if 240 #end if
241 use_raw=$method.use_raw, 241 use_raw=$method.use_raw,
242 #if str($method.layout) != 'None'
243 layout='$method.layout', 242 layout='$method.layout',
244 #end if
245 edges=$method.edges.edges, 243 edges=$method.edges.edges,
246 #if str($method.edges.edges) == 'True' 244 #if str($method.edges.edges) == 'True'
247 edges_width=$method.edges.edges_width, 245 edges_width=$method.edges.edges_width,
248 edges_color='$method.edges.edges_color', 246 edges_color='$method.edges.edges_color',
249 #end if 247 #end if
402 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option> 400 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
403 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option> 401 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
404 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option> 402 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
405 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option> 403 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
406 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option> 404 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
405 <!-- doesn't currenty work: https://github.com/galaxyproject/tools-iuc/pull/3485#issuecomment-800055967
407 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option> 406 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
407 -->
408 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option> 408 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
409 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option> 409 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
410 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option> 410 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
411 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option> 411 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
412 </param> 412 </param>
637 </when> 637 </when>
638 <when value="pl.draw_graph"> 638 <when value="pl.draw_graph">
639 <expand macro="param_color"/> 639 <expand macro="param_color"/>
640 <expand macro="gene_symbols"/> 640 <expand macro="gene_symbols"/>
641 <expand macro="param_use_raw"/> 641 <expand macro="param_use_raw"/>
642 <param argument="layout" type="select" optional="true" label="Plotting layout" help=""> 642 <param argument="layout" type="select" optional="false" label="Plotting layout" help="">
643 <expand macro="options_layout"/> 643 <expand macro="options_layout"/>
644 </param> 644 </param>
645 <expand macro="pl_edges"/> 645 <expand macro="pl_edges"/>
646 <expand macro="param_arrows"/> 646 <expand macro="param_arrows"/>
647 <expand macro="param_sort_order"/> 647 <expand macro="param_sort_order"/>
812 <has_text_matching expression="projection='2d'"/> 812 <has_text_matching expression="projection='2d'"/>
813 <has_text_matching expression="legend_loc='right margin'"/> 813 <has_text_matching expression="legend_loc='right margin'"/>
814 <has_text_matching expression="legend_fontsize=1"/> 814 <has_text_matching expression="legend_fontsize=1"/>
815 <has_text_matching expression="legend_fontweight='normal'"/> 815 <has_text_matching expression="legend_fontweight='normal'"/>
816 <has_text_matching expression="color_map='inferno'"/> 816 <has_text_matching expression="color_map='inferno'"/>
817 <has_text_matching expression="palette='inferno'"/>
818 <has_text_matching expression="frameon=True"/> 817 <has_text_matching expression="frameon=True"/>
819 <has_text_matching expression="size=1.0"/> 818 <has_text_matching expression="size=1.0"/>
820 </assert_contents> 819 </assert_contents>
821 </output> 820 </output>
822 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> 821 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
860 <has_text_matching expression="sort_order=True"/> 859 <has_text_matching expression="sort_order=True"/>
861 <has_text_matching expression="projection='2d'"/> 860 <has_text_matching expression="projection='2d'"/>
862 <has_text_matching expression="legend_loc='right margin'"/> 861 <has_text_matching expression="legend_loc='right margin'"/>
863 <has_text_matching expression="legend_fontsize=1"/> 862 <has_text_matching expression="legend_fontsize=1"/>
864 <has_text_matching expression="legend_fontweight='normal'"/> 863 <has_text_matching expression="legend_fontweight='normal'"/>
865 <has_text_matching expression="palette='bwr'"/>
866 <has_text_matching expression="frameon=False"/> 864 <has_text_matching expression="frameon=False"/>
867 <has_text_matching expression="size=1.0"/> 865 <has_text_matching expression="size=1.0"/>
868 <has_text_matching expression="title='A title'"/> 866 <has_text_matching expression="title='A title'"/>
869 </assert_contents> 867 </assert_contents>
870 </output> 868 </output>
1027 <has_text_matching expression="scale='width'"/> 1025 <has_text_matching expression="scale='width'"/>
1028 <has_text_matching expression="bw='scott'"/> 1026 <has_text_matching expression="bw='scott'"/>
1029 <has_text_matching expression="scale='width'"/> 1027 <has_text_matching expression="scale='width'"/>
1030 <has_text_matching expression="linewidth=0.0"/> 1028 <has_text_matching expression="linewidth=0.0"/>
1031 <has_text_matching expression="color='AliceBlue'"/> 1029 <has_text_matching expression="color='AliceBlue'"/>
1032 <has_text_matching expression="palette='viridis'"/>
1033 <has_text_matching expression="saturation=0.75"/> 1030 <has_text_matching expression="saturation=0.75"/>
1034 </assert_contents> 1031 </assert_contents>
1035 </output> 1032 </output>
1036 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/> 1033 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
1037 </test> 1034 </test>
1065 <param name="standard_scale" value="None"/> 1062 <param name="standard_scale" value="None"/>
1066 <section name="seaborn_violinplot"> 1063 <section name="seaborn_violinplot">
1067 <param name="bw" value="scott"/> 1064 <param name="bw" value="scott"/>
1068 <param name="linewidth" value="0"/> 1065 <param name="linewidth" value="0"/>
1069 <param name="color" value="AliceBlue"/> 1066 <param name="color" value="AliceBlue"/>
1070 <param name="palette" value="viridis"/>
1071 <param name="saturation" value="0.75"/> 1067 <param name="saturation" value="0.75"/>
1072 </section> 1068 </section>
1073 </conditional> 1069 </conditional>
1074 <section name="advanced_common"> 1070 <section name="advanced_common">
1075 <param name="show_log" value="true" /> 1071 <param name="show_log" value="true" />
1089 <has_text_matching expression="scale='width'"/> 1085 <has_text_matching expression="scale='width'"/>
1090 <has_text_matching expression="bw='scott'"/> 1086 <has_text_matching expression="bw='scott'"/>
1091 <has_text_matching expression="scale='width'"/> 1087 <has_text_matching expression="scale='width'"/>
1092 <has_text_matching expression="linewidth=0.0"/> 1088 <has_text_matching expression="linewidth=0.0"/>
1093 <has_text_matching expression="color='AliceBlue'"/> 1089 <has_text_matching expression="color='AliceBlue'"/>
1094 <has_text_matching expression="palette='viridis'"/>
1095 <has_text_matching expression="saturation=0.75"/> 1090 <has_text_matching expression="saturation=0.75"/>
1096 </assert_contents> 1091 </assert_contents>
1097 </output> 1092 </output>
1098 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/> 1093 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
1099 </test> 1094 </test>
1537 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 1532 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
1538 <param name="format" value="png"/> 1533 <param name="format" value="png"/>
1539 <conditional name="method"> 1534 <conditional name="method">
1540 <param name="method" value="pl.draw_graph"/> 1535 <param name="method" value="pl.draw_graph"/>
1541 <param name="use_raw" value="false"/> 1536 <param name="use_raw" value="false"/>
1537 <param name="layout" value="fr"/>
1542 <conditional name="edges"> 1538 <conditional name="edges">
1543 <param name="edges" value="True"/> 1539 <param name="edges" value="True"/>
1544 <param name="edges_width" value="0.1"/> 1540 <param name="edges_width" value="0.1"/>
1545 <param name="edges_color" value="Crimson"/> 1541 <param name="edges_color" value="Crimson"/>
1546 </conditional> 1542 </conditional>
1677 <has_text_matching expression="sharey=True"/> 1673 <has_text_matching expression="sharey=True"/>
1678 </assert_contents> 1674 </assert_contents>
1679 </output> 1675 </output>
1680 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1676 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1681 </test> 1677 </test>
1682 <test> 1678 <!-- test 20: pl.rank_genes_groups_violin, currently broken
1683 <!-- test 20: pl.rank_genes_groups_violin !--> 1679 <test>
1684 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1680 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1685 <param name="format" value="png"/> 1681 <param name="format" value="png"/>
1686 <conditional name="method"> 1682 <conditional name="method">
1687 <param name="method" value="pl.rank_genes_groups_violin"/> 1683 <param name="method" value="pl.rank_genes_groups_violin"/>
1688 <conditional name="genes"> 1684 <conditional name="genes">
1721 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/> 1717 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
1722 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/> 1718 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
1723 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/> 1719 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1724 </output_collection> 1720 </output_collection>
1725 </test> 1721 </test>
1722 -->
1726 <test> 1723 <test>
1727 <!-- test 21: pl.rank_genes_groups_dotplot !--> 1724 <!-- test 21: pl.rank_genes_groups_dotplot !-->
1728 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> 1725 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
1729 <param name="format" value="png"/> 1726 <param name="format" value="png"/>
1730 <conditional name="method"> 1727 <conditional name="method">
1873 <has_text_matching expression="scale='width'"/> 1870 <has_text_matching expression="scale='width'"/>
1874 <has_text_matching expression="bw='scott'"/> 1871 <has_text_matching expression="bw='scott'"/>
1875 <has_text_matching expression="scale='width'"/> 1872 <has_text_matching expression="scale='width'"/>
1876 <has_text_matching expression="linewidth=0.0"/> 1873 <has_text_matching expression="linewidth=0.0"/>
1877 <has_text_matching expression="color='AliceBlue'"/> 1874 <has_text_matching expression="color='AliceBlue'"/>
1878 <has_text_matching expression="palette='viridis'"/>
1879 <has_text_matching expression="saturation=0.75"/> 1875 <has_text_matching expression="saturation=0.75"/>
1880 </assert_contents> 1876 </assert_contents>
1881 </output> 1877 </output>
1882 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/> 1878 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
1883 </test> 1879 </test>