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comparison plot.xml @ 20:387671174a49 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy commit 732303de9670376c88e7afb2f23336ee1433e97d
author iuc
date Thu, 26 Mar 2026 12:48:53 +0000
parents fc222791d03c
children
comparison
equal deleted inserted replaced
19:fc222791d03c 20:387671174a49
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="bio_tools"/> 5 <expand macro="bio_tools"/>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.9.1">matplotlib</requirement> 7 <requirement type="package" version="2.3.3">pandas</requirement>
8 <requirement type="package" version="0.13.2">seaborn</requirement>
9 <requirement type="package" version="0.11.6">python-igraph</requirement> 8 <requirement type="package" version="0.11.6">python-igraph</requirement>
9 <requirement type="package" version="0.0.9">easy_vitessce</requirement>
10 <requirement type="package" version="0.51.0">starlette</requirement>
11 <requirement type="package" version="0.2.7">kerchunk</requirement>
12 <requirement type="package" version="0.9.21">anywidget</requirement>
13 <requirement type="package" version="0.40.0">uvicorn</requirement>
10 </expand> 14 </expand>
11 <stdio> 15 <stdio>
12 <regex match="... storing" source="stderr" level="warning"/> 16 <regex match="... storing" source="stderr" level="warning"/>
13 </stdio> 17 </stdio>
14 <expand macro="version_command"/> 18 <expand macro="version_command"/>
19 <configfile name="script_file"><![CDATA[ 23 <configfile name="script_file"><![CDATA[
20 @CMD_IMPORTS@ 24 @CMD_IMPORTS@
21 @CMD_READ_INPUTS@ 25 @CMD_READ_INPUTS@
22 26
23 sc.settings.figdir = '.' 27 sc.settings.figdir = '.'
28
29 #if str($method.method) in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and $method.interactive_plot:
30 @VITESSCE_ACTIVATE@
31 #end if
24 32
25 #if str($method.method) == 'pl.scatter': 33 #if str($method.method) == 'pl.scatter':
26 34
27 #if str($method.type.type) == 'xy': 35 #if str($method.type.type) == 'xy':
28 x_field='$method.type.x' 36 x_field='$method.type.x'
84 @CMD_PARAM_TITLE@ 92 @CMD_PARAM_TITLE@
85 @CMD_SHOW_NONE@) 93 @CMD_SHOW_NONE@)
86 94
87 #else if str($method.method) == 'pl.heatmap': 95 #else if str($method.method) == 'pl.heatmap':
88 @CMD_VAR_NAMES_HEADER_CHECK@ 96 @CMD_VAR_NAMES_HEADER_CHECK@
97 #if $method.interactive_plot:
98 vitessce_widget = sc.pl.heatmap(
99 #else:
89 sc.pl.heatmap( 100 sc.pl.heatmap(
101 #end if
90 @CMD_PARAM_PLOT_INPUTS@ 102 @CMD_PARAM_PLOT_INPUTS@
91 @CMD_PARAMS_INPUTS@ 103 @CMD_PARAMS_INPUTS@
92 @CMD_PARAM_GENE_SYMBOLS@ 104 @CMD_PARAM_GENE_SYMBOLS@
93 @CMD_PARAMS_PLOTS@ 105 @CMD_PARAMS_PLOTS@
94 @CMD_PARAMS_PL_HEATMAP@ 106 @CMD_PARAMS_PL_HEATMAP@
95 @CMD_SHOW_NONE@) 107 @CMD_SHOW_NONE@)
96 108
97 #else if str($method.method) == 'pl.dotplot': 109 #else if str($method.method) == 'pl.dotplot':
98 @CMD_VAR_NAMES_HEADER_CHECK@ 110 @CMD_VAR_NAMES_HEADER_CHECK@
111 #if $method.interactive_plot:
112 vitessce_widget = sc.pl.dotplot(
113 #else:
99 sc.pl.dotplot( 114 sc.pl.dotplot(
115 #end if
100 @CMD_PARAM_PLOT_INPUTS@ 116 @CMD_PARAM_PLOT_INPUTS@
101 @CMD_PARAMS_INPUTS@ 117 @CMD_PARAMS_INPUTS@
102 @CMD_PARAM_GENE_SYMBOLS@ 118 @CMD_PARAM_GENE_SYMBOLS@
103 @CMD_PARAMS_PLOTS@ 119 @CMD_PARAMS_PLOTS@
104 @CMD_PL_DOTPLOT@ 120 @CMD_PL_DOTPLOT@
112 @CMD_PARAM_GENE_SYMBOLS@ 128 @CMD_PARAM_GENE_SYMBOLS@
113 @CMD_PARAMS_PLOTS@ 129 @CMD_PARAMS_PLOTS@
114 @CMD_SHOW_NONE@) 130 @CMD_SHOW_NONE@)
115 131
116 #else if str($method.method) == 'pl.violin': 132 #else if str($method.method) == 'pl.violin':
133 #if $method.interactive_plot:
134 vitessce_widget = sc.pl.violin(
135 #else:
117 sc.pl.violin( 136 sc.pl.violin(
137 #end if
118 @CMD_PARAM_PLOT_INPUTS@ 138 @CMD_PARAM_PLOT_INPUTS@
119 #if str($method.key_variables.type) == 'var_names': 139 #if str($method.key_variables.type) == 'var_names':
120 #set $key_list = adata.var_names 140 #set $key_list = adata.var_names
121 #else if str($method.key_variables.type) == 'obs': 141 #else if str($method.key_variables.type) == 'obs':
122 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns 142 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
218 @CMD_PARAMS_FIGSIZE@ 238 @CMD_PARAMS_FIGSIZE@
219 save='.$format', 239 save='.$format',
220 @CMD_SHOW_NONE@) 240 @CMD_SHOW_NONE@)
221 241
222 #else if str($method.method) == 'pl.pca': 242 #else if str($method.method) == 'pl.pca':
243 #if $method.interactive_plot:
244 vitessce_widget = sc.pl.pca(
245 #else:
223 sc.pl.pca( 246 sc.pl.pca(
247 #end if
224 @CMD_PARAM_PLOT_INPUTS@ 248 @CMD_PARAM_PLOT_INPUTS@
225 @CMD_PARAM_COLOR@ 249 @CMD_PARAM_COLOR@
226 @CMD_PARAM_GENE_SYMBOLS@ 250 @CMD_PARAM_GENE_SYMBOLS@
227 use_raw=$method.use_raw, 251 use_raw=$method.use_raw,
228 sort_order=$method.sort_order, 252 sort_order=$method.sort_order,
262 @CMD_SCATTER_OUTINE@ 286 @CMD_SCATTER_OUTINE@
263 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ 287 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
264 @CMD_SHOW_NONE@) 288 @CMD_SHOW_NONE@)
265 289
266 #else if str($method.method) == 'pl.tsne': 290 #else if str($method.method) == 'pl.tsne':
291 #if $method.interactive_plot:
292 vitessce_widget = sc.pl.tsne(
293 #else:
267 sc.pl.tsne( 294 sc.pl.tsne(
295 #end if
268 @CMD_PARAM_PLOT_INPUTS@ 296 @CMD_PARAM_PLOT_INPUTS@
269 @CMD_PARAM_COLOR@ 297 @CMD_PARAM_COLOR@
270 @CMD_PARAM_GENE_SYMBOLS@ 298 @CMD_PARAM_GENE_SYMBOLS@
271 use_raw=$method.use_raw, 299 use_raw=$method.use_raw,
272 @CMD_PL_EDGES@ 300 @CMD_PL_EDGES@
276 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@ 304 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
277 @CMD_SCATTER_OUTINE@ 305 @CMD_SCATTER_OUTINE@
278 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ 306 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
279 @CMD_PARAM_LAYER@ 307 @CMD_PARAM_LAYER@
280 @CMD_SHOW_NONE@) 308 @CMD_SHOW_NONE@)
281
282 #else if str($method.method) == 'pl.umap': 309 #else if str($method.method) == 'pl.umap':
310 #if $method.interactive_plot:
311 vitessce_widget = sc.pl.umap(
312 #else:
283 sc.pl.umap( 313 sc.pl.umap(
314 #end if
284 @CMD_PARAM_PLOT_INPUTS@ 315 @CMD_PARAM_PLOT_INPUTS@
285 @CMD_PARAM_COLOR@ 316 @CMD_PARAM_COLOR@
286 @CMD_PARAM_GENE_SYMBOLS@ 317 @CMD_PARAM_GENE_SYMBOLS@
287 use_raw=$method.use_raw, 318 use_raw=$method.use_raw,
288 @CMD_PL_EDGES@ 319 @CMD_PL_EDGES@
294 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ 325 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
295 @CMD_PARAM_LAYER@ 326 @CMD_PARAM_LAYER@
296 @CMD_SHOW_NONE@) 327 @CMD_SHOW_NONE@)
297 328
298 #else if str($method.method) == 'pl.diffmap': 329 #else if str($method.method) == 'pl.diffmap':
330 #if $method.interactive_plot:
331 vitessce_widget = sc.pl.diffmap(
332 #else:
299 sc.pl.diffmap( 333 sc.pl.diffmap(
334 #end if
300 @CMD_PARAM_PLOT_INPUTS@ 335 @CMD_PARAM_PLOT_INPUTS@
301 @CMD_PARAM_COLOR@ 336 @CMD_PARAM_COLOR@
302 @CMD_PARAM_GENE_SYMBOLS@ 337 @CMD_PARAM_GENE_SYMBOLS@
303 use_raw=$method.use_raw, 338 use_raw=$method.use_raw,
304 sort_order=$method.sort_order, 339 sort_order=$method.sort_order,
348 ncols=$method.ncols, 383 ncols=$method.ncols,
349 wspace=$method.wspace, 384 wspace=$method.wspace,
350 hspace=$method.hspace, 385 hspace=$method.hspace,
351 @CMD_SHOW_NONE@) 386 @CMD_SHOW_NONE@)
352 387
353
354
355 #else if str($method.method) == 'pl.dpt_timeseries': 388 #else if str($method.method) == 'pl.dpt_timeseries':
356 sc.pl.dpt_timeseries( 389 sc.pl.dpt_timeseries(
357 @CMD_PARAM_PLOT_INPUTS@ 390 @CMD_PARAM_PLOT_INPUTS@
358 #if str($method.heatmap.as_heatmap) == 'True' 391 #if str($method.heatmap.as_heatmap) == 'True'
359 #if $method.heatmap.color_map 392 #if $method.heatmap.color_map
502 @CMD_PARAMS_PL_HEATMAP@ 535 @CMD_PARAMS_PL_HEATMAP@
503 @CMD_SHOW_NONE@) 536 @CMD_SHOW_NONE@)
504 537
505 #end if 538 #end if
506 539
507 #if $advanced_common.output_anndata: 540 #if $advanced_common.output_anndata or (str($method.method) in ['pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and $method.interactive_plot):
508 @CMD_ANNDATA_WRITE_OUTPUTS@ 541 @CMD_ANNDATA_WRITE_OUTPUTS@
542 #end if
543
544 #if str($method.method) in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and $method.interactive_plot:
545 @VITESSCE_CONFIG@
509 #end if 546 #end if
510 547
511 ]]></configfile> 548 ]]></configfile>
512 </configfiles> 549 </configfiles>
513 <inputs> 550 <inputs>
533 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option> 570 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
534 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option> 571 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
535 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option> 572 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
536 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option> 573 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
537 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option> 574 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
538 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
539 <!-- <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> -->
540 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option> 575 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
541 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option> 576 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
542 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option> 577 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
543 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option> 578 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
544 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option> 579 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
612 <expand macro="param_title"/> 647 <expand macro="param_title"/>
613 </section> 648 </section>
614 </when> 649 </when>
615 <when value="pl.heatmap"> 650 <when value="pl.heatmap">
616 <expand macro="params_inputs"/> 651 <expand macro="params_inputs"/>
652 <expand macro="param_interactive_plot"/>
617 <expand macro="param_gene_symbols"/> 653 <expand macro="param_gene_symbols"/>
618 <expand macro="params_plots"/> 654 <expand macro="params_plots"/>
619 <expand macro="params_pl_heatmap"/> 655 <expand macro="params_pl_heatmap"/>
620 </when> 656 </when>
621 <when value="pl.dotplot"> 657 <when value="pl.dotplot">
622 <expand macro="params_inputs"/> 658 <expand macro="params_inputs"/>
659 <expand macro="param_interactive_plot"/>
623 <expand macro="param_gene_symbols"/> 660 <expand macro="param_gene_symbols"/>
624 <expand macro="params_plots"/> 661 <expand macro="params_plots"/>
625 <expand macro="params_pl_dotplot"/> 662 <expand macro="params_pl_dotplot"/>
626 </when> 663 </when>
627 <when value="pl.tracksplot"> 664 <when value="pl.tracksplot">
628 <expand macro="params_inputs"/> 665 <expand macro="params_inputs"/>
629 <expand macro="param_gene_symbols"/> 666 <expand macro="param_gene_symbols"/>
630 <expand macro="params_plots"/> 667 <expand macro="params_plots"/>
631 </when> 668 </when>
632 <when value="pl.violin"> 669 <when value="pl.violin">
670 <expand macro="param_interactive_plot"/>
633 <conditional name="key_variables"> 671 <conditional name="key_variables">
634 <param name="type" type="select" label="Keys for accessing variables"> 672 <param name="type" type="select" label="Keys for accessing variables">
635 <option value="var_names" selected="true">All variables in '.var_names'</option> 673 <option value="var_names" selected="true">All variables in '.var_names'</option>
636 <option value="obs">All fields in '.obs'</option> 674 <option value="obs">All fields in '.obs'</option>
637 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option> 675 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
744 <option value="logit">logit</option> 782 <option value="logit">logit</option>
745 </param> 783 </param>
746 <expand macro="pl_figsize"/> 784 <expand macro="pl_figsize"/>
747 </when> 785 </when>
748 <when value="pl.pca"> 786 <when value="pl.pca">
787 <expand macro="param_interactive_plot"/>
749 <expand macro="param_color"/> 788 <expand macro="param_color"/>
750 <expand macro="param_gene_symbols"/> 789 <expand macro="param_gene_symbols"/>
751 <expand macro="param_use_raw"/> 790 <expand macro="param_use_raw"/>
752 <expand macro="param_sort_order"/> 791 <expand macro="param_sort_order"/>
753 <expand macro="param_groups"/> 792 <expand macro="param_groups"/>
775 <expand macro="params_pl_attribute_section"/> 814 <expand macro="params_pl_attribute_section"/>
776 <expand macro="params_scatter_outine"/> 815 <expand macro="params_scatter_outine"/>
777 <expand macro="section_matplotlib_pyplot_scatter"/> 816 <expand macro="section_matplotlib_pyplot_scatter"/>
778 </when> 817 </when>
779 <when value="pl.tsne"> 818 <when value="pl.tsne">
819 <expand macro="param_interactive_plot"/>
780 <expand macro="param_color"/> 820 <expand macro="param_color"/>
781 <expand macro="param_gene_symbols"/> 821 <expand macro="param_gene_symbols"/>
782 <expand macro="param_use_raw"/> 822 <expand macro="param_use_raw"/>
783 <expand macro="pl_edges"/> 823 <expand macro="pl_edges"/>
784 <expand macro="param_arrows"/> 824 <expand macro="param_arrows"/>
788 <expand macro="params_scatter_outine"/> 828 <expand macro="params_scatter_outine"/>
789 <expand macro="section_matplotlib_pyplot_scatter"/> 829 <expand macro="section_matplotlib_pyplot_scatter"/>
790 <expand macro="param_layer"/> 830 <expand macro="param_layer"/>
791 </when> 831 </when>
792 <when value="pl.umap"> 832 <when value="pl.umap">
833 <expand macro="param_interactive_plot"/>
793 <expand macro="param_color"/> 834 <expand macro="param_color"/>
794 <expand macro="param_gene_symbols"/> 835 <expand macro="param_gene_symbols"/>
795 <expand macro="param_use_raw"/> 836 <expand macro="param_use_raw"/>
796 <expand macro="pl_edges"/> 837 <expand macro="pl_edges"/>
797 <expand macro="param_arrows"/> 838 <expand macro="param_arrows"/>
801 <expand macro="params_scatter_outine"/> 842 <expand macro="params_scatter_outine"/>
802 <expand macro="section_matplotlib_pyplot_scatter"/> 843 <expand macro="section_matplotlib_pyplot_scatter"/>
803 <expand macro="param_layer"/> 844 <expand macro="param_layer"/>
804 </when> 845 </when>
805 <when value="pl.diffmap"> 846 <when value="pl.diffmap">
847 <expand macro="param_interactive_plot"/>
806 <expand macro="param_color"/> 848 <expand macro="param_color"/>
807 <expand macro="param_gene_symbols"/> 849 <expand macro="param_gene_symbols"/>
808 <expand macro="param_use_raw"/> 850 <expand macro="param_use_raw"/>
809 <expand macro="param_sort_order"/> 851 <expand macro="param_sort_order"/>
810 <expand macro="param_groups"/> 852 <expand macro="param_groups"/>
848 <param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/> 890 <param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/>
849 <expand macro="param_ncols"/> 891 <expand macro="param_ncols"/>
850 <expand macro="param_wspace"/> 892 <expand macro="param_wspace"/>
851 <expand macro="param_hspace"/> 893 <expand macro="param_hspace"/>
852 </when> 894 </when>
853 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
854 <!-- <when value="pl.dpt_groups_pseudotime">
855 <expand macro="param_color_map"/>
856 </when> -->
857 <when value="pl.dpt_timeseries"> 895 <when value="pl.dpt_timeseries">
858 <conditional name="heatmap"> 896 <conditional name="heatmap">
859 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?"> 897 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?">
860 <option value="True" selected="true">Yes</option> 898 <option value="True" selected="true">Yes</option>
861 <option value="False">No</option> 899 <option value="False">No</option>
982 <param name="output_anndata" type="boolean" checked="false" label="Output annotated data matrix?"/> 1020 <param name="output_anndata" type="boolean" checked="false" label="Output annotated data matrix?"/>
983 </expand> 1021 </expand>
984 </inputs> 1022 </inputs>
985 <outputs> 1023 <outputs>
986 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}"> 1024 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
987 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter> 1025 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin' and not (method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot'])</filter>
988 </data> 1026 </data>
989 <collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}"> 1027 <collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}">
990 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/> 1028 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).png" format="png"/>
991 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 1029 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
992 </collection> 1030 </collection>
993 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}"> 1031 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
994 <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter> 1032 <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin' and not (method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot'])</filter>
995 </data> 1033 </data>
996 <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}"> 1034 <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}">
997 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/> 1035 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).pdf" format="pdf"/>
998 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 1036 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
999 </collection> 1037 </collection>
1000 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}"> 1038 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
1001 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter> 1039 <filter>format == 'svg' and method['method'] != 'pl.rank_genes_groups_violin' and not (method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot'])</filter>
1002 </data> 1040 </data>
1003 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}"> 1041 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
1004 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/> 1042 <discover_datasets pattern="rank_genes_groups_(?P&lt;designation&gt;.*).svg" format="svg"/>
1005 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 1043 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
1006 </collection> 1044 </collection>
1007 <data name="hidden_output" format="txt" label="Log file" hidden="true" > 1045 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
1008 <filter>advanced_common['show_log']</filter> 1046 <filter>advanced_common['show_log']</filter>
1009 </data> 1047 </data>
1010 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"> 1048 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
1011 <filter>advanced_common['output_anndata']</filter> 1049 <filter>advanced_common['output_anndata'] or (method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot'])</filter>
1050 </data>
1051 <data name="vitessce_config" format="vitessce.json" from_work_dir="config.json" label="${tool.name} (${method.method}) on ${on_string}: Vitessce interactive visualization">
1052 <filter>method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot']</filter>
1053 </data>
1054 <data name="anndata_config" format="json" from_work_dir="anndata.ref.json" label="${tool.name} (${method.method}) on ${on_string}: Anndata configuration">
1055 <filter>method['method'] in ['pl.pca', 'pl.umap', 'pl.tsne', 'pl.diffmap', 'pl.violin', 'pl.dotplot', 'pl.heatmap'] and method['interactive_plot']</filter>
1012 </data> 1056 </data>
1013 </outputs> 1057 </outputs>
1014 <tests> 1058 <tests>
1015 <!-- test 1 --> 1059 <!-- test 1 -->
1016 <test expect_num_outputs="2"> 1060 <test expect_num_outputs="2">
1053 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/> 1097 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
1054 </test> 1098 </test>
1055 1099
1056 <!-- test 2 --> 1100 <!-- test 2 -->
1057 <test expect_num_outputs="2"> 1101 <test expect_num_outputs="2">
1058 <param name="adata" value="krumsiek11.h5ad"/> 1102 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1059 <param name="format" value="png"/> 1103 <param name="format" value="png"/>
1060 <conditional name="method"> 1104 <conditional name="method">
1061 <param name="method" value="pl.scatter"/> 1105 <param name="method" value="pl.scatter"/>
1062 <conditional name="type"> 1106 <conditional name="type">
1063 <param name="type" value="xy"/> 1107 <param name="type" value="xy"/>
1064 <param name="x" value="EKLF"/> 1108 <param name="x" value="FCGRT"/>
1065 <param name="y" value="Cebpa"/> 1109 <param name="y" value="SAT1"/>
1066 </conditional> 1110 </conditional>
1067 <section name="plot"> 1111 <section name="plot">
1068 <param name="legend_fontsize" value="1"/> 1112 <param name="legend_fontsize" value="1"/>
1069 <param name="legend_fontweight" value="normal"/> 1113 <param name="legend_fontweight" value="normal"/>
1070 <param name="palette" value="bwr"/> 1114 <param name="palette" value="bwr"/>
1076 <param name="show_log" value="true"/> 1120 <param name="show_log" value="true"/>
1077 </section> 1121 </section>
1078 <output name="hidden_output"> 1122 <output name="hidden_output">
1079 <assert_contents> 1123 <assert_contents>
1080 <has_text_matching expression="sc.pl.scatter"/> 1124 <has_text_matching expression="sc.pl.scatter"/>
1081 <has_text_matching expression="x_field='EKLF'"/> 1125 <has_text_matching expression="x_field='FCGRT'"/>
1082 <has_text_matching expression="y_field='Cebpa'"/> 1126 <has_text_matching expression="y_field='SAT1'"/>
1083 <has_text_matching expression="use_raw=None"/> 1127 <has_text_matching expression="use_raw=None"/>
1084 <has_text_matching expression="sort_order=True"/> 1128 <has_text_matching expression="sort_order=True"/>
1085 <has_text_matching expression="projection='2d'"/> 1129 <has_text_matching expression="projection='2d'"/>
1086 <has_text_matching expression="legend_fontsize=1"/> 1130 <has_text_matching expression="legend_fontsize=1"/>
1087 <has_text_matching expression="legend_fontweight='normal'"/> 1131 <has_text_matching expression="legend_fontweight='normal'"/>
1088 <has_text_matching expression="frameon=True"/> 1132 <has_text_matching expression="frameon=True"/>
1089 <has_text_matching expression="size=1.0"/> 1133 <has_text_matching expression="size=1.0"/>
1090 <has_text_matching expression="title='A title'"/> 1134 <has_text_matching expression="title='A title'"/>
1091 </assert_contents> 1135 </assert_contents>
1092 </output> 1136 </output>
1093 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/> 1137 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
1094 </test> 1138 </test>
1095 1139
1096 <!-- test 3 --> 1140 <!-- test 3 -->
1097 <test expect_num_outputs="2"> 1141 <test expect_num_outputs="2">
1098 <param name="adata" value="pbmc68k_reduced.h5ad"/> 1142 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1126 <has_text_matching expression="frameon=True"/> 1170 <has_text_matching expression="frameon=True"/>
1127 <has_text_matching expression="size=1.0"/> 1171 <has_text_matching expression="size=1.0"/>
1128 <has_text_matching expression="title='A title'"/> 1172 <has_text_matching expression="title='A title'"/>
1129 </assert_contents> 1173 </assert_contents>
1130 </output> 1174 </output>
1131 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="image_diff"/> 1175 <output name="out_png" file="pl.scatter.pbmc68k_reduced_n_genes_n_counts.png" ftype="png" compare="image_diff"/>
1132 </test> 1176 </test>
1133 1177
1134 <!-- test 4 --> 1178 <!-- test 4 -->
1135 <test expect_num_outputs="2"> 1179 <test expect_num_outputs="2">
1136 <param name="adata" value="krumsiek11.h5ad"/> 1180 <param name="adata" value="krumsiek11.h5ad"/>
1906 </assert_contents> 1950 </assert_contents>
1907 </output> 1951 </output>
1908 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/> 1952 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
1909 </test> 1953 </test>
1910 1954
1911 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
1912 <!-- test 27 --> 1955 <!-- test 27 -->
1913 <!-- <test expect_num_outputs="2">
1914 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1915 <param name="format" value="png"/>
1916 <conditional name="method">
1917 <param name="method" value="pl.dpt_groups_pseudotime"/>
1918
1919 </conditional>
1920 <section name="advanced_common">
1921 <param name="show_log" value="true"/>
1922 </section>
1923 <output name="hidden_output">
1924 <assert_contents>
1925 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
1926 <has_text_matching expression="color_map='viridis'"/>
1927 </assert_contents>
1928 </output>
1929 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1930 </test> -->
1931
1932 <!-- test 28 -->
1933 <test expect_num_outputs="2"> 1956 <test expect_num_outputs="2">
1934 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 1957 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1935 <param name="format" value="png"/> 1958 <param name="format" value="png"/>
1936 <conditional name="method"> 1959 <conditional name="method">
1937 <param name="method" value="pl.dpt_timeseries"/> 1960 <param name="method" value="pl.dpt_timeseries"/>
1946 </assert_contents> 1969 </assert_contents>
1947 </output> 1970 </output>
1948 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1971 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1949 </test> 1972 </test>
1950 1973
1951 <!-- test 29 --> 1974 <!-- test 28 -->
1952 <test expect_num_outputs="2"> 1975 <test expect_num_outputs="2">
1953 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/> 1976 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
1954 <param name="format" value="png"/> 1977 <param name="format" value="png"/>
1955 <conditional name="method"> 1978 <conditional name="method">
1956 <param name="method" value="pl.paga"/> 1979 <param name="method" value="pl.paga"/>
1969 <has_h5_keys keys="uns/paga"/> 1992 <has_h5_keys keys="uns/paga"/>
1970 </assert_contents> 1993 </assert_contents>
1971 </output> 1994 </output>
1972 </test> 1995 </test>
1973 1996
1974 <!-- test 30 --> 1997 <!-- test 29 -->
1975 <test expect_num_outputs="1"> 1998 <test expect_num_outputs="1">
1976 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/> 1999 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
1977 <param name="format" value="png"/> 2000 <param name="format" value="png"/>
1978 <conditional name="method"> 2001 <conditional name="method">
1979 <param name="method" value="pl.paga_compare"/> 2002 <param name="method" value="pl.paga_compare"/>
1984 <param name="edge_width_scale" value="5"/> 2007 <param name="edge_width_scale" value="5"/>
1985 </conditional> 2008 </conditional>
1986 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/> 2009 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
1987 </test> 2010 </test>
1988 2011
1989 <!-- test 31 --> 2012 <!-- test 30 -->
1990 <!-- <test expect_num_outputs="2"> 2013 <!-- <test expect_num_outputs="2">
1991 test pl.paga_path 2014 test pl.paga_path
1992 </test> --> 2015 </test> -->
1993 2016
1994 <!-- test 32 --> 2017 <!-- test 30 -->
1995 <test expect_num_outputs="2"> 2018 <test expect_num_outputs="2">
1996 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2019 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1997 <param name="format" value="png"/> 2020 <param name="format" value="png"/>
1998 <conditional name="method"> 2021 <conditional name="method">
1999 <param name="method" value="pl.rank_genes_groups"/> 2022 <param name="method" value="pl.rank_genes_groups"/>
2011 </assert_contents> 2034 </assert_contents>
2012 </output> 2035 </output>
2013 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2036 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2014 </test> 2037 </test>
2015 2038
2016 <!-- test 33 --> 2039 <!-- test 31 -->
2017 <test expect_num_outputs="2"> 2040 <test expect_num_outputs="2">
2018 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2041 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2019 <param name="format" value="png"/> 2042 <param name="format" value="png"/>
2020 <conditional name="method"> 2043 <conditional name="method">
2021 <param name="method" value="pl.rank_genes_groups_violin"/> 2044 <param name="method" value="pl.rank_genes_groups_violin"/>
2046 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/> 2069 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/>
2047 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/> 2070 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>
2048 </output_collection> 2071 </output_collection>
2049 </test> 2072 </test>
2050 2073
2051 <!-- test 34 --> 2074 <!-- test 32 -->
2052 <test expect_num_outputs="2"> 2075 <test expect_num_outputs="2">
2053 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2076 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2054 <param name="format" value="png"/> 2077 <param name="format" value="png"/>
2055 <conditional name="method"> 2078 <conditional name="method">
2056 <param name="method" value="pl.rank_genes_groups_stacked_violin"/> 2079 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
2088 </assert_contents> 2111 </assert_contents>
2089 </output> 2112 </output>
2090 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/> 2113 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>
2091 </test> 2114 </test>
2092 2115
2093 <!-- test 35 --> 2116 <!-- test 33 -->
2094 <test expect_num_outputs="2"> 2117 <test expect_num_outputs="2">
2095 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2118 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2096 <param name="format" value="png"/> 2119 <param name="format" value="png"/>
2097 <conditional name="method"> 2120 <conditional name="method">
2098 <param name="method" value="pl.rank_genes_groups_heatmap"/> 2121 <param name="method" value="pl.rank_genes_groups_heatmap"/>
2114 </assert_contents> 2137 </assert_contents>
2115 </output> 2138 </output>
2116 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2139 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2117 </test> 2140 </test>
2118 2141
2119 <!-- test 36 --> 2142 <!-- test 34 -->
2120 <test expect_num_outputs="2"> 2143 <test expect_num_outputs="2">
2121 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2144 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2122 <param name="format" value="png"/> 2145 <param name="format" value="png"/>
2123 <conditional name="method"> 2146 <conditional name="method">
2124 <param name="method" value="pl.rank_genes_groups_dotplot"/> 2147 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2137 </assert_contents> 2160 </assert_contents>
2138 </output> 2161 </output>
2139 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2162 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2140 </test> 2163 </test>
2141 2164
2142 <!-- test 37 --> 2165 <!-- test 35 -->
2143 <test expect_num_outputs="2"> 2166 <test expect_num_outputs="2">
2144 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2167 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2145 <param name="format" value="png"/> 2168 <param name="format" value="png"/>
2146 <conditional name="method"> 2169 <conditional name="method">
2147 <param name="method" value="pl.rank_genes_groups_matrixplot"/> 2170 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
2162 </assert_contents> 2185 </assert_contents>
2163 </output> 2186 </output>
2164 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2187 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2165 </test> 2188 </test>
2166 2189
2167 <!-- test 38 pl.rank_genes_groups_dotplot with marker list--> 2190 <!-- test 36 pl.rank_genes_groups_dotplot with marker list-->
2168 <test expect_num_outputs="2"> 2191 <test expect_num_outputs="2">
2169 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> 2192 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2170 <param name="format" value="png"/> 2193 <param name="format" value="png"/>
2171 <conditional name="method"> 2194 <conditional name="method">
2172 <param name="method" value="pl.rank_genes_groups_dotplot"/> 2195 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2187 </assert_contents> 2210 </assert_contents>
2188 </output> 2211 </output>
2189 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/> 2212 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>
2190 </test> 2213 </test>
2191 2214
2192 <!-- test 39: pl.rank_genes_groups_dotplot with marker list --> 2215 <!-- test 37: pl.rank_genes_groups_dotplot with marker list -->
2193 <test expect_num_outputs="2"> 2216 <test expect_num_outputs="2">
2194 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> 2217 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2195 <param name="format" value="png"/> 2218 <param name="format" value="png"/>
2196 <conditional name="method"> 2219 <conditional name="method">
2197 <param name="method" value="pl.rank_genes_groups_dotplot"/> 2220 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2212 </assert_contents> 2235 </assert_contents>
2213 </output> 2236 </output>
2214 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/> 2237 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
2215 </test> 2238 </test>
2216 2239
2240 <!-- test 38 -->
2241 <test expect_num_outputs="2">
2242 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2243 <param name="format" value="png"/>
2244 <conditional name="method">
2245 <param name="method" value="pl.rank_genes_groups_tracksplot"/>
2246 </conditional>
2247 <section name="advanced_common">
2248 <param name="show_log" value="true" />
2249 </section>
2250 <output name="hidden_output">
2251 <assert_contents>
2252 <has_text_matching expression="sc.pl.rank_genes_groups_tracksplot"/>
2253 </assert_contents>
2254 </output>
2255 <output name="out_png" file="pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
2256 </test>
2257
2258 <!-- test 39 -->
2259 <test expect_num_outputs="4">
2260 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
2261 <param name="format" value="png"/>
2262 <conditional name="method">
2263 <param name="method" value="pl.umap"/>
2264 <param name="interactive_plot" value="true"/>
2265 <param name="color" value="paul15_clusters"/>
2266 <param name="gene_symbols" value="symbol"/>
2267 <conditional name="edges">
2268 <param name="edges" value="True"/>
2269 </conditional>
2270 <section name="plot">
2271 <param name="legend_fontsize" value="1"/>
2272 <param name="legend_fontweight" value="normal"/>
2273 <param name="size" value="1"/>
2274 </section>
2275 </conditional>
2276 <section name="advanced_common">
2277 <param name="show_log" value="true"/>
2278 </section>
2279 <output name="hidden_output">
2280 <assert_contents>
2281 <has_text_matching expression="sc.pl.umap"/>
2282 <has_text_matching expression="color=\['paul15_clusters'\]"/>
2283 <has_text_matching expression="use_raw=False"/>
2284 <has_text_matching expression="edges=True"/>
2285 <has_text_matching expression="edges_width=0.1"/>
2286 <has_text_matching expression="arrows=False"/>
2287 <has_text_matching expression="sort_order=True"/>
2288 <has_text_matching expression="projection='2d'"/>
2289 <has_text_matching expression="legend_loc='right margin'"/>
2290 <has_text_matching expression="legend_fontsize=1"/>
2291 <has_text_matching expression="legend_fontweight='normal'"/>
2292 <has_text_matching expression="size=1.0"/>
2293 <has_text_matching expression="frameon=True"/>
2294 <has_text_matching expression="ncols=4"/>
2295 <has_text_matching expression="wspace=0.1"/>
2296 <has_text_matching expression="hspace=0.25"/>
2297 <has_text_matching expression="gene_symbols='symbol'"/>
2298 </assert_contents>
2299 </output>
2300 <output name="vitessce_config">
2301 <assert_contents>
2302 <has_n_lines n="93" />
2303 <has_text_matching expression="sc.pl.embedding for UMAP"/>
2304 <has_text_matching expression="anndata.h5ad"/>
2305 <has_text_matching expression="scatterplot"/>
2306 </assert_contents>
2307 </output>
2308 <output name="anndata_config">
2309 <assert_contents>
2310 <has_n_lines n="1" />
2311 <has_size value="29779" delta="100" />
2312 <has_text_matching expression="\\&quot;zarr_format\\&quot;:2"/>
2313 </assert_contents>
2314 </output>
2315 </test>
2316
2217 <!-- test 40 --> 2317 <!-- test 40 -->
2218 <test expect_num_outputs="2"> 2318 <test expect_num_outputs="4">
2219 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> 2319 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2220 <param name="format" value="png"/> 2320 <param name="format" value="png"/>
2221 <conditional name="method"> 2321 <conditional name="method">
2222 <param name="method" value="pl.rank_genes_groups_tracksplot"/> 2322 <param name="method" value="pl.dotplot"/>
2223 </conditional> 2323 <param name="interactive_plot" value="true"/>
2224 <section name="advanced_common"> 2324 <conditional name="var_names">
2225 <param name="show_log" value="true" /> 2325 <param name="type" value="custom"/>
2226 </section> 2326 <param name="var_names" value="Fog1,EKLF,SCL"/>
2227 <output name="hidden_output"> 2327 </conditional>
2228 <assert_contents> 2328 <param name="gene_symbols" value="symbol"/>
2229 <has_text_matching expression="sc.pl.rank_genes_groups_tracksplot"/> 2329 <param name="groupby" value="cell_type"/>
2230 </assert_contents> 2330 <param name="dendrogram" value="True"/>
2231 </output> 2331 <param name="color_map" value="YlGnBu"/>
2232 <output name="out_png" file="pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/> 2332 </conditional>
2333 <section name="advanced_common">
2334 <param name="show_log" value="true"/>
2335 </section>
2336 <output name="hidden_output">
2337 <assert_contents>
2338 <has_text_matching expression="sc.pl.dotplot"/>
2339 <has_text_matching expression="gene_symbols='symbol'"/>
2340 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2341 <has_text_matching expression="groupby='cell_type'"/>
2342 <has_text_matching expression="log=False"/>
2343 <has_text_matching expression="use_raw=None"/>
2344 <has_text_matching expression="num_categories=7"/>
2345 <has_text_matching expression="dendrogram=True"/>
2346 </assert_contents>
2347 </output>
2348 <output name="vitessce_config">
2349 <assert_contents>
2350 <has_n_lines n="98" />
2351 <has_text_matching expression="sc.pl.dotplot"/>
2352 <has_text_matching expression="anndata.h5ad"/>
2353 </assert_contents>
2354 </output>
2355 <output name="anndata_config">
2356 <assert_contents>
2357 <has_n_lines n="1" />
2358 <has_size value="12217" delta="100" />
2359 <has_text_matching expression="\\&quot;zarr_format\\&quot;:2"/>
2360 </assert_contents>
2361 </output>
2233 </test> 2362 </test>
2234 </tests> 2363 </tests>
2235 <help><![CDATA[ 2364 <help><![CDATA[
2236 Generic: Scatter plot along observations or variables axes (`pl.scatter`) 2365 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
2237 ========================================================================= 2366 =========================================================================
2410 ============================================================================================== 2539 ==============================================================================================
2411 2540
2412 More details on the `scanpy documentation 2541 More details on the `scanpy documentation
2413 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.embedding_density.html>`__ 2542 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.embedding_density.html>`__
2414 2543
2415 .. This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed.
2416 .. Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
2417 .. ===========================================================================================================
2418
2419 .. More details on the `scanpy documentation
2420 .. <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__
2421
2422 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`) 2544 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
2423 ===================================================================================================== 2545 =====================================================================================================
2424 2546
2425 More details on the `scanpy documentation 2547 More details on the `scanpy documentation
2426 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__ 2548 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__