Mercurial > repos > goeckslab > squidpy
comparison squidpy_spatial.xml @ 1:bad34051dc8a draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 130ef7e8ae6cab35866b72617e53d35acc11475a
| author | goeckslab |
|---|---|
| date | Wed, 28 Feb 2024 20:52:29 +0000 |
| parents | be0e7952e229 |
| children | 4a058bd23a12 |
comparison
equal
deleted
inserted
replaced
| 0:be0e7952e229 | 1:bad34051dc8a |
|---|---|
| 1 <tool id="squidpy_spatial" name="Squidpy Graph and Plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="squidpy_spatial" name="Analyze and visualize spatial multi-omics data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>for spatial analysis </description> | 2 <description>with Squidpy</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>main_macros.xml</import> | 4 <import>main_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <edam_operations> | |
| 7 <edam_operation>operation_3443</edam_operation> | |
| 8 </edam_operations> | |
| 6 <expand macro="squidpy_requirements"/> | 9 <expand macro="squidpy_requirements"/> |
| 7 <expand macro="macro_stdio" /> | 10 <expand macro="macro_stdio" /> |
| 8 <version_command>echo "@TOOL_VERSION@"</version_command> | 11 <version_command>echo "@TOOL_VERSION@"</version_command> |
| 9 <command> | 12 <command detect_errors="aggressive"> |
| 10 <![CDATA[ | 13 <![CDATA[ |
| 11 python '$__tool_directory__/squidpy_spatial.py' | 14 python '$__tool_directory__/squidpy_spatial.py' |
| 12 --inputs '$inputs' | 15 --inputs '$inputs' |
| 13 --anndata '$anndata' | 16 --anndata '$anndata' |
| 14 --output '$output' | 17 --output '$output' |
| 255 <data from_work_dir="image.png" format="png" name="output_plot" label="Squidpy.pl.${analyses.selected_tool} on ${on_string}" > | 258 <data from_work_dir="image.png" format="png" name="output_plot" label="Squidpy.pl.${analyses.selected_tool} on ${on_string}" > |
| 256 <filter>analyses['selected_tool'] in ['nhood_enrichment', 'centrality_scores', 'interaction_matrix', 'ligrec', 'ripley', 'co_occurrence']</filter> | 259 <filter>analyses['selected_tool'] in ['nhood_enrichment', 'centrality_scores', 'interaction_matrix', 'ligrec', 'ripley', 'co_occurrence']</filter> |
| 257 </data> | 260 </data> |
| 258 </outputs> | 261 </outputs> |
| 259 <tests> | 262 <tests> |
| 260 <test> | 263 <test expect_num_outputs="1"> |
| 261 <param name="anndata" value="imc.h5ad" ftype="h5ad" /> | 264 <param name="anndata" value="imc.h5ad" ftype="h5ad" /> |
| 262 <param name="selected_tool" value="spatial_neighbors" /> | 265 <param name="selected_tool" value="spatial_neighbors" /> |
| 263 <output name="output"> | 266 <output name="output"> |
| 264 <assert_contents> | 267 <assert_contents> |
| 265 <has_h5_keys keys="uns/spatial_neighbors" /> | 268 <has_h5_keys keys="uns/spatial_neighbors" /> |
| 266 </assert_contents> | 269 </assert_contents> |
| 267 </output> | 270 </output> |
| 268 </test> | 271 </test> |
| 269 <test> | 272 <test expect_num_outputs="2"> |
| 270 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> | 273 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
| 271 <param name="selected_tool" value="nhood_enrichment" /> | 274 <param name="selected_tool" value="nhood_enrichment" /> |
| 272 <param name="cluster_key" value="cell type" /> | 275 <param name="cluster_key" value="cell type" /> |
| 273 <output name="output"> | 276 <output name="output"> |
| 274 <assert_contents> | 277 <assert_contents> |
| 275 <has_h5_keys keys="uns/cell type_nhood_enrichment" /> | 278 <has_h5_keys keys="uns/cell type_nhood_enrichment" /> |
| 276 </assert_contents> | 279 </assert_contents> |
| 277 </output> | 280 </output> |
| 278 <output name="output_plot" file="imc_nhood_enrichment.png" compare="sim_size" delta="2000" /> | 281 <output name="output_plot" file="imc_nhood_enrichment.png" compare="sim_size" delta="2000" /> |
| 279 </test> | 282 </test> |
| 280 <test> | 283 <test expect_num_outputs="2"> |
| 281 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> | 284 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
| 282 <param name="selected_tool" value="co_occurrence" /> | 285 <param name="selected_tool" value="co_occurrence" /> |
| 283 <param name="cluster_key" value="cell type" /> | 286 <param name="cluster_key" value="cell type" /> |
| 284 <output name="output"> | 287 <output name="output"> |
| 285 <assert_contents> | 288 <assert_contents> |
| 286 <has_h5_keys keys="uns/cell type_co_occurrence" /> | 289 <has_h5_keys keys="uns/cell type_co_occurrence" /> |
| 287 </assert_contents> | 290 </assert_contents> |
| 288 </output> | 291 </output> |
| 289 <output name="output_plot" file="imc_co_occurrence.png" compare="sim_size" delta="2000" /> | 292 <output name="output_plot" file="imc_co_occurrence.png" compare="sim_size" delta="2000" /> |
| 290 </test> | 293 </test> |
| 291 <test> | 294 <test expect_num_outputs="2"> |
| 292 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> | 295 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
| 293 <param name="selected_tool" value="centrality_scores" /> | 296 <param name="selected_tool" value="centrality_scores" /> |
| 294 <param name="cluster_key" value="cell type" /> | 297 <param name="cluster_key" value="cell type" /> |
| 295 <output name="output"> | 298 <output name="output"> |
| 296 <assert_contents> | 299 <assert_contents> |
| 297 <has_h5_keys keys="uns/cell type_centrality_scores" /> | 300 <has_h5_keys keys="uns/cell type_centrality_scores" /> |
| 298 </assert_contents> | 301 </assert_contents> |
| 299 </output> | 302 </output> |
| 300 <output name="output_plot" file="imc_centrality_scores.png" compare="sim_size" delta="2000" /> | 303 <output name="output_plot" file="imc_centrality_scores.png" compare="sim_size" delta="2000" /> |
| 301 </test> | 304 </test> |
| 302 <test> | 305 <test expect_num_outputs="2"> |
| 303 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> | 306 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
| 304 <param name="selected_tool" value="interaction_matrix" /> | 307 <param name="selected_tool" value="interaction_matrix" /> |
| 305 <param name="cluster_key" value="cell type" /> | 308 <param name="cluster_key" value="cell type" /> |
| 306 <output name="output"> | 309 <output name="output"> |
| 307 <assert_contents> | 310 <assert_contents> |
| 308 <has_h5_keys keys="uns/cell type_interactions" /> | 311 <has_h5_keys keys="uns/cell type_interactions" /> |
| 309 </assert_contents> | 312 </assert_contents> |
| 310 </output> | 313 </output> |
| 311 <output name="output_plot" file="imc_interaction_matrix.png" compare="sim_size" delta="2000" /> | 314 <output name="output_plot" file="imc_interaction_matrix.png" compare="sim_size" delta="2000" /> |
| 312 </test> | 315 </test> |
| 313 <test> | 316 <test expect_num_outputs="2"> |
| 314 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> | 317 <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" /> |
| 315 <param name="selected_tool" value="ripley" /> | 318 <param name="selected_tool" value="ripley" /> |
| 316 <param name="cluster_key" value="cell type" /> | 319 <param name="cluster_key" value="cell type" /> |
| 317 <output name="output"> | 320 <output name="output"> |
| 318 <assert_contents> | 321 <assert_contents> |
| 339 *Plotting (PNG) if applicable* | 342 *Plotting (PNG) if applicable* |
| 340 | 343 |
| 341 | 344 |
| 342 ]]> | 345 ]]> |
| 343 </help> | 346 </help> |
| 344 <citations> | 347 <expand macro="citations" /> |
| 345 </citations> | |
| 346 </tool> | 348 </tool> |