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comparison plot.xml @ 16:1072ce66b426 draft

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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
comparison
equal deleted inserted replaced
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