Mercurial > repos > iuc > scanpy_plot
comparison plot.xml @ 16:1072ce66b426 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0
| author | iuc |
|---|---|
| date | Tue, 20 Aug 2024 09:53:51 +0000 |
| parents | f7446fd8d5e7 |
| children | 2dfb2227a16c |
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| 15:70fa84e99463 | 16:1072ce66b426 |
|---|---|
| 77 @CMD_param_title@ | 77 @CMD_param_title@ |
| 78 @CMD_param_size@ | 78 @CMD_param_size@ |
| 79 frameon=$method.plot.frameon) | 79 frameon=$method.plot.frameon) |
| 80 | 80 |
| 81 #else if $method.method == 'pl.heatmap' | 81 #else if $method.method == 'pl.heatmap' |
| 82 @CMD_var_names_header_check@ | |
| 82 sc.pl.heatmap( | 83 sc.pl.heatmap( |
| 83 @CMD_param_plot_inputs@ | 84 @CMD_param_plot_inputs@ |
| 84 #if $method.gene_symbols | 85 #if $method.gene_symbols |
| 85 gene_symbols='$method.gene_symbols', | 86 gene_symbols='$method.gene_symbols', |
| 86 #end if | 87 #end if |
| 87 @CMD_params_inputs@ | 88 @CMD_params_inputs@ |
| 88 @CMD_params_plots@ | 89 @CMD_params_plots@ |
| 89 @CMD_pl_heatmap@) | 90 @CMD_pl_heatmap@) |
| 90 | 91 |
| 91 #else if $method.method == 'pl.dotplot' | 92 #else if $method.method == 'pl.dotplot' |
| 93 @CMD_var_names_header_check@ | |
| 92 sc.pl.dotplot( | 94 sc.pl.dotplot( |
| 93 @CMD_param_plot_inputs@ | 95 @CMD_param_plot_inputs@ |
| 94 #if $method.gene_symbols | 96 #if $method.gene_symbols |
| 95 gene_symbols='$method.gene_symbols', | 97 gene_symbols='$method.gene_symbols', |
| 96 #end if | 98 #end if |
| 127 rotation=$method.rotation, | 129 rotation=$method.rotation, |
| 128 #end if | 130 #end if |
| 129 @CMD_params_seaborn_violinplot@) | 131 @CMD_params_seaborn_violinplot@) |
| 130 | 132 |
| 131 #else if $method.method == 'pl.stacked_violin' | 133 #else if $method.method == 'pl.stacked_violin' |
| 134 @CMD_var_names_header_check@ | |
| 132 sc.pl.stacked_violin( | 135 sc.pl.stacked_violin( |
| 133 @CMD_param_plot_inputs@ | 136 @CMD_param_plot_inputs@ |
| 134 #if $method.gene_symbols | 137 #if $method.gene_symbols |
| 135 gene_symbols='$method.gene_symbols', | 138 gene_symbols='$method.gene_symbols', |
| 136 #end if | 139 #end if |
| 137 @CMD_params_inputs@ | 140 @CMD_params_inputs@ |
| 138 @CMD_params_plots@ | 141 @CMD_params_plots@ |
| 139 @CMD_pl_stacked_violin@) | 142 @CMD_pl_stacked_violin@) |
| 140 | 143 |
| 141 #else if $method.method == 'pl.matrixplot' | 144 #else if $method.method == 'pl.matrixplot' |
| 145 @CMD_var_names_header_check@ | |
| 142 sc.pl.matrixplot( | 146 sc.pl.matrixplot( |
| 143 @CMD_param_plot_inputs@ | 147 @CMD_param_plot_inputs@ |
| 144 #if $method.gene_symbols | 148 #if $method.gene_symbols |
| 145 gene_symbols='$method.gene_symbols', | 149 gene_symbols='$method.gene_symbols', |
| 146 #end if | 150 #end if |
| 397 #end if | 401 #end if |
| 398 #end if | 402 #end if |
| 399 scale='$method.violin_plot.scale') | 403 scale='$method.violin_plot.scale') |
| 400 | 404 |
| 401 #else if $method.method == 'pl.rank_genes_groups_dotplot' | 405 #else if $method.method == 'pl.rank_genes_groups_dotplot' |
| 406 | |
| 407 @CMD_var_names_header_check@ | |
| 408 | |
| 402 sc.pl.rank_genes_groups_dotplot( | 409 sc.pl.rank_genes_groups_dotplot( |
| 403 @CMD_param_plot_inputs@ | 410 @CMD_param_plot_inputs@ |
| 404 @CMD_pl_rank_genes_groups_ext@ | 411 #if $method.var_names.type == 'custom' |
| 412 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')]) | |
| 413 var_names=$var_names, | |
| 414 #else if $method.var_names.type == 'customfile' | |
| 415 var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()}, | |
| 416 #else | |
| 417 n_genes=$method.n_genes, | |
| 418 #end if | |
| 419 #if $method.groupby != '' | |
| 420 groupby='$method.groupby', | |
| 421 #end if | |
| 422 num_categories=$method.num_categories, | |
| 423 #if $method.key != '' | |
| 424 key='$method.key', | |
| 425 #end if | |
| 405 #if $method.gene_symbols | 426 #if $method.gene_symbols |
| 406 gene_symbols='$method.gene_symbols', | 427 gene_symbols='$method.gene_symbols', |
| 407 #end if | 428 #end if |
| 408 @CMD_params_plots@ | 429 @CMD_params_plots@ |
| 409 @CMD_pl_dotplot@) | 430 @CMD_pl_dotplot@) |
| 817 <expand macro="conditional_stripplot"/> | 838 <expand macro="conditional_stripplot"/> |
| 818 <expand macro="param_scale"/> | 839 <expand macro="param_scale"/> |
| 819 </section> | 840 </section> |
| 820 </when> | 841 </when> |
| 821 <when value="pl.rank_genes_groups_dotplot"> | 842 <when value="pl.rank_genes_groups_dotplot"> |
| 843 <expand macro="params_inputs"/> | |
| 822 <expand macro="pl_rank_genes_groups_ext"/> | 844 <expand macro="pl_rank_genes_groups_ext"/> |
| 823 <expand macro="params_plots"/> | 845 <expand macro="params_plots"/> |
| 824 <expand macro="gene_symbols"/> | 846 <expand macro="gene_symbols"/> |
| 825 <expand macro="pl_dotplot"/> | 847 <expand macro="pl_dotplot"/> |
| 826 </when> | 848 </when> |
| 2031 <param name="format" value="png"/> | 2053 <param name="format" value="png"/> |
| 2032 <conditional name="method"> | 2054 <conditional name="method"> |
| 2033 <param name="method" value="pl.rank_genes_groups_dotplot"/> | 2055 <param name="method" value="pl.rank_genes_groups_dotplot"/> |
| 2034 <param name="gene_symbols" value="symbol"/> | 2056 <param name="gene_symbols" value="symbol"/> |
| 2035 <param name="n_genes" value="10"/> | 2057 <param name="n_genes" value="10"/> |
| 2058 <conditional name="var_names"> | |
| 2059 <param name="type" value="all"/> | |
| 2060 </conditional> | |
| 2036 <param name="log" value="False"/> | 2061 <param name="log" value="False"/> |
| 2037 <param name="use_raw" value="False"/> | 2062 <param name="use_raw" value="False"/> |
| 2038 <param name="dendrogram" value="False"/> | 2063 <param name="dendrogram" value="False"/> |
| 2039 <param name="color_map" value="viridis"/> | 2064 <param name="color_map" value="viridis"/> |
| 2040 <section name="matplotlib_pyplot_scatter"> | 2065 <section name="matplotlib_pyplot_scatter"> |
| 2231 <has_text_matching expression="title='A title'"/> | 2256 <has_text_matching expression="title='A title'"/> |
| 2232 </assert_contents> | 2257 </assert_contents> |
| 2233 </output> | 2258 </output> |
| 2234 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> | 2259 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/> |
| 2235 </test> | 2260 </test> |
| 2261 <test expect_num_outputs="2"> | |
| 2262 <!-- test 35: pl.rank_genes_groups_dotplot with marker list --> | |
| 2263 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> | |
| 2264 <param name="format" value="png"/> | |
| 2265 <conditional name="method"> | |
| 2266 <param name="method" value="pl.rank_genes_groups_dotplot"/> | |
| 2267 <conditional name="var_names"> | |
| 2268 <param name="type" value="customfile"/> | |
| 2269 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/> | |
| 2270 </conditional> | |
| 2271 <param name="groupby" value="bulk_labels"/> | |
| 2272 <param name="log" value="False"/> | |
| 2273 <param name="use_raw" value="False"/> | |
| 2274 <param name="dendrogram" value="False"/> | |
| 2275 <param name="color_map" value="viridis"/> | |
| 2276 <section name="matplotlib_pyplot_scatter"> | |
| 2277 <param name="linewidths" value="0" /> | |
| 2278 <param name="edgecolors" value="face"/> | |
| 2279 </section> | |
| 2280 </conditional> | |
| 2281 <section name="advanced_common"> | |
| 2282 <param name="show_log" value="true" /> | |
| 2283 </section> | |
| 2284 <output name="hidden_output"> | |
| 2285 <assert_contents> | |
| 2286 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/> | |
| 2287 <has_text_matching expression="groupby='bulk_labels'"/> | |
| 2288 <has_text_matching expression="log=False"/> | |
| 2289 <has_text_matching expression="use_raw=False"/> | |
| 2290 <has_text_matching expression="dendrogram=False"/> | |
| 2291 <has_text_matching expression="color_map='viridis'"/> | |
| 2292 <has_text_matching expression="lw=0.0"/> | |
| 2293 <has_text_matching expression="ec='face'"/> | |
| 2294 </assert_contents> | |
| 2295 </output> | |
| 2296 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="sim_size"/> | |
| 2297 </test> | |
| 2298 <test expect_num_outputs="2"> | |
| 2299 <!-- test 36: pl.rank_genes_groups_dotplot with marker list --> | |
| 2300 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> | |
| 2301 <param name="format" value="png"/> | |
| 2302 <conditional name="method"> | |
| 2303 <param name="method" value="pl.rank_genes_groups_dotplot"/> | |
| 2304 <conditional name="var_names"> | |
| 2305 <param name="type" value="customfile"/> | |
| 2306 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/> | |
| 2307 </conditional> | |
| 2308 <param name="groupby" value="bulk_labels"/> | |
| 2309 <param name="log" value="False"/> | |
| 2310 <param name="use_raw" value="False"/> | |
| 2311 <param name="dendrogram" value="False"/> | |
| 2312 <param name="color_map" value="viridis"/> | |
| 2313 <section name="matplotlib_pyplot_scatter"> | |
| 2314 <param name="linewidths" value="0" /> | |
| 2315 <param name="edgecolors" value="face"/> | |
| 2316 </section> | |
| 2317 </conditional> | |
| 2318 <section name="advanced_common"> | |
| 2319 <param name="show_log" value="true" /> | |
| 2320 </section> | |
| 2321 <output name="hidden_output"> | |
| 2322 <assert_contents> | |
| 2323 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/> | |
| 2324 <has_text_matching expression="groupby='bulk_labels'"/> | |
| 2325 <has_text_matching expression="log=False"/> | |
| 2326 <has_text_matching expression="use_raw=False"/> | |
| 2327 <has_text_matching expression="dendrogram=False"/> | |
| 2328 <has_text_matching expression="color_map='viridis'"/> | |
| 2329 <has_text_matching expression="lw=0.0"/> | |
| 2330 <has_text_matching expression="ec='face'"/> | |
| 2331 </assert_contents> | |
| 2332 </output> | |
| 2333 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="sim_size"/> | |
| 2334 </test> | |
| 2236 </tests> | 2335 </tests> |
| 2237 <help><![CDATA[ | 2336 <help><![CDATA[ |
| 2238 Generic: Scatter plot along observations or variables axes (`pl.scatter`) | 2337 Generic: Scatter plot along observations or variables axes (`pl.scatter`) |
| 2239 ========================================================================= | 2338 ========================================================================= |
| 2240 | 2339 |