Mercurial > repos > iuc > episcanpy_cluster_embed

comparison cluster_embed.xml @ 1:51dbb534fbce draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470
author iuc
date Sat, 22 Apr 2023 12:13:18 +0000
parents 43711b22f28b
children
comparison
equal deleted inserted replaced
0:43711b22f28b 1:51dbb534fbce
44 copy=False, 44 copy=False,
45 method='$method.rank_features_method', 45 method='$method.rank_features_method',
46 corr_method='$method.rank_features_corr_method' 46 corr_method='$method.rank_features_corr_method'
47 ) 47 )
48 48
49 #else if $method.method == 'tl.find_genes'
50 esc.tl.find_genes(
51 adata,
52 gtf_file='$method.find_genes_gtf_file',
53 key_added='$method.find_genes_key_added',
54 upstream=$method.find_genes_upstream,
55 feature_type='$method.find_genes_feature_type',
56 annotation='$method.find_genes_annotation',
57 raw=$method.find_genes_raw)
58
59 #else if $method.method == 'tl.get_n_clusters' 49 #else if $method.method == 'tl.get_n_clusters'
60 esc.tl.getNClusters( 50 esc.tl.getNClusters(
61 adata, 51 adata,
62 n_cluster=$method.get_n_clusters_n_cluster, 52 n_cluster=$method.get_n_clusters_n_cluster,
63 range_min=$method.get_n_clusters_range_min, 53 range_min=$method.get_n_clusters_range_min,
86 <expand macro="inputs_anndata"/> 76 <expand macro="inputs_anndata"/>
87 <conditional name="method"> 77 <conditional name="method">
88 <param argument="method" type="select" label="Method used for Clustering or Embedding"> 78 <param argument="method" type="select" label="Method used for Clustering or Embedding">
89 <option value="pp.lazy">Embedding: Automatically compute PCA coordinates, loadings and variance decomposition, a neighborhood graph of observations, t-distributed stochastic neighborhood embedding (tSNE) Uniform Manifold Approximation and Projection (UMAP), using 'pp.lazy'</option> 79 <option value="pp.lazy">Embedding: Automatically compute PCA coordinates, loadings and variance decomposition, a neighborhood graph of observations, t-distributed stochastic neighborhood embedding (tSNE) Uniform Manifold Approximation and Projection (UMAP), using 'pp.lazy'</option>
90 <option value="tl.rank_features">Rank features for characterizing groups, using 'tl.rank_features'</option> 80 <option value="tl.rank_features">Rank features for characterizing groups, using 'tl.rank_features'</option>
91 <option value="tl.find_genes">Embedding: Find genes and add annotations, using 'pp.find_genes'</option>
92 <option value="tl.get_n_clusters">Clustering: Test different settings of louvain to obtain the target number of clusters, using 'tl.getNClusters'</option> 81 <option value="tl.get_n_clusters">Clustering: Test different settings of louvain to obtain the target number of clusters, using 'tl.getNClusters'</option>
93 <option value="tl.kmeans">Clustering: Compute kmeans clustering using X_pca fits, using 'tl.kmeans'</option> 82 <option value="tl.kmeans">Clustering: Compute kmeans clustering using X_pca fits, using 'tl.kmeans'</option>
94 <option value="tl.hc">Clustering: Compute hierarchical clustering using X_pca fits, using 'tl.hc'</option> 83 <option value="tl.hc">Clustering: Compute hierarchical clustering using X_pca fits, using 'tl.hc'</option>
95 </param> 84 </param>
96 <when value="pp.lazy"> 85 <when value="pp.lazy">
211 <param name="rank_features_corr_method" value="benjamini-hochberg" type="select" label="p-value correction method" help="(corr_method)"> 200 <param name="rank_features_corr_method" value="benjamini-hochberg" type="select" label="p-value correction method" help="(corr_method)">
212 <option value="benjamini-hochberg">Benjamini Hochberg</option> 201 <option value="benjamini-hochberg">Benjamini Hochberg</option>
213 <option value="bonferroni">Bonferroni</option> 202 <option value="bonferroni">Bonferroni</option>
214 </param> 203 </param>
215 </when> 204 </when>
216 <when value="tl.find_genes">
217 <param name="find_genes_gtf_file" type="data" format="gtf" label="Annotation GTF file" help="(gtf_file)"/>
218 <param name="find_genes_key_added" value="transcript_annotation" type="text" label="Key added" help="(key_added)">
219 <sanitizer invalid_char="">
220 <valid initial="string.letters,string.digits">
221 <add value="_" />
222 <add value="-" />
223 <add value="." />
224 <add value=" " />
225 <add value="," />
226 </valid>
227 </sanitizer>
228 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
229 </param>
230 <param name="find_genes_upstream" value="2000" min="0" type="integer" label="Upstream" help="(upstream)"/>
231 <param name="find_genes_feature_type" value="transcript" type="text" label="Feature type" help="(feature_type)">
232 <sanitizer invalid_char="">
233 <valid initial="string.letters,string.digits">
234 <add value="_" />
235 <add value="-" />
236 <add value="." />
237 <add value=" " />
238 <add value="," />
239 </valid>
240 </sanitizer>
241 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
242 </param>
243 <param name="find_genes_annotation" value="HAVANA" type="text" label="Annotation" help="(annotation)">
244 <sanitizer invalid_char="">
245 <valid initial="string.letters,string.digits">
246 <add value="_" />
247 <add value="-" />
248 <add value="." />
249 <add value=" " />
250 <add value="," />
251 </valid>
252 </sanitizer>
253 <validator type="regex">[0-9a-zA-Z_., -]+</validator>
254 </param>
255 <param name="find_genes_raw" type="select" label="Raw?" help="(raw)">
256 <option value="True">True</option>
257 <option value="False" selected="true">False</option>
258 </param>
259 </when>
260 <when value="tl.get_n_clusters"> 205 <when value="tl.get_n_clusters">
261 <param name="get_n_clusters_n_cluster" value="14" min="1" type="integer" label="Number of clusters" help="(n_cluster)"/> 206 <param name="get_n_clusters_n_cluster" value="14" min="1" type="integer" label="Number of clusters" help="(n_cluster)"/>
262 <param name="get_n_clusters_method" type="select" label="Clustering method to use" help="(method)"> 207 <param name="get_n_clusters_method" type="select" label="Clustering method to use" help="(method)">
263 <option value="leiden" selected="true">leiden</option> 208 <option value="leiden" selected="true">leiden</option>
264 <option value="louvain">louvain</option> 209 <option value="louvain">louvain</option>
291 <outputs> 236 <outputs>
292 <expand macro="anndata_outputs"/> 237 <expand macro="anndata_outputs"/>
293 </outputs> 238 </outputs>
294 <tests> 239 <tests>
295 <test expect_num_outputs="2"> 240 <test expect_num_outputs="2">
296 <!-- test 0- pp.lazy --> 241 <!-- pp.lazy -->
297 <param name="adata" value="krumsiek11.h5ad" /> 242 <param name="adata" value="krumsiek11.h5ad" />
298 <conditional name="method"> 243 <conditional name="method">
299 <param name="method" value="pp.lazy"/> 244 <param name="method" value="pp.lazy"/>
300 <param name="lazy_pp_pca" value="True"/> 245 <param name="lazy_pp_pca" value="True"/>
301 <param name="lazy_svd_solver" value="arpack"/> 246 <param name="lazy_svd_solver" value="arpack"/>
320 </assert_contents> 265 </assert_contents>
321 </output> 266 </output>
322 <output name="anndata_out" file="krumsiek11.pp.lazy.h5ad" ftype="h5ad" compare="sim_size"/> 267 <output name="anndata_out" file="krumsiek11.pp.lazy.h5ad" ftype="h5ad" compare="sim_size"/>
323 </test> 268 </test>
324 <test expect_num_outputs="2"> 269 <test expect_num_outputs="2">
325 <!-- test 1- tl.rank_features --> 270 <!-- tl.rank_features -->
326 <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" /> 271 <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" />
327 <conditional name="method"> 272 <conditional name="method">
328 <param name="method" value="tl.rank_features"/> 273 <param name="method" value="tl.rank_features"/>
329 <param name="rank_features_groupby" value="louvain"/> 274 <param name="rank_features_groupby" value="louvain"/>
330 <param name="rank_features_use_raw" value="False"/> 275 <param name="rank_features_use_raw" value="False"/>
343 <assert_contents> 288 <assert_contents>
344 <has_h5_keys keys="obs, uns, obsm, varm, obsp" /> 289 <has_h5_keys keys="obs, uns, obsm, varm, obsp" />
345 </assert_contents> 290 </assert_contents>
346 </output> 291 </output>
347 </test> 292 </test>
348 <test expect_num_outputs="2"> 293 <test expect_num_outputs="2">
349 <!-- test 2-tl.find_genes --> 294 <!-- tl.get_n_clusters -->
350 <param name="adata" value="chrY.h5ad" />
351 <conditional name="method">
352 <param name="method" value="tl.find_genes"/>
353 <param name="find_genes_gtf_file" value="chrY.gtf"/>
354 <param name="find_genes_key_added" value="transcript_annotation"/>
355 <param name="find_genes_upstream" value="2000"/>
356 <param name="find_genes_feature_type" value="transcript"/>
357 <param name="find_genes_annotation" value="HAVANA"/>
358 <param name="find_genes_raw" value="False"/>
359 </conditional>
360 <section name="advanced_common">
361 <param name="show_log" value="true" />
362 </section>
363 <output name="anndata_out" file="chrY_with_transcript_annotation.h5ad" ftype="h5ad" compare="sim_size">
364 <assert_contents>
365 <has_h5_keys keys="var" />
366 </assert_contents>
367 </output>
368 </test>
369 <test expect_num_outputs="2">
370 <!-- test 3-tl.get_n_clusters -->
371 <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" /> 295 <param name="adata" value="krumsiek11.pp.lazy.tl.louvain.h5ad" />
372 <conditional name="method"> 296 <conditional name="method">
373 <param name="method" value="tl.get_n_clusters"/> 297 <param name="method" value="tl.get_n_clusters"/>
374 <param name="get_n_clusters_n_clusters" value="3"/> 298 <param name="get_n_clusters_n_clusters" value="3"/>
375 <param name="get_n_clusters_method" value="louvain"/> 299 <param name="get_n_clusters_method" value="louvain"/>
384 <param name="show_log" value="true" /> 308 <param name="show_log" value="true" />
385 </section> 309 </section>
386 <output name="anndata_out" file="krumsiek11.tl.get_n_clusters.h5ad" ftype="h5ad"/> 310 <output name="anndata_out" file="krumsiek11.tl.get_n_clusters.h5ad" ftype="h5ad"/>
387 </test> 311 </test>
388 <test expect_num_outputs="2"> 312 <test expect_num_outputs="2">
389 <!-- test 4-tl.kmeans --> 313 <!-- tl.kmeans -->
390 <param name="adata" value="krumsiek11.pp.lazy.h5ad" /> 314 <param name="adata" value="krumsiek11.pp.lazy.h5ad" />
391 <conditional name="method"> 315 <conditional name="method">
392 <param name="method" value="tl.kmeans"/> 316 <param name="method" value="tl.kmeans"/>
393 <param name="kmeans_num_clusters" value="14"/> 317 <param name="kmeans_num_clusters" value="14"/>
394 </conditional> 318 </conditional>
396 <param name="show_log" value="true" /> 320 <param name="show_log" value="true" />
397 </section> 321 </section>
398 <output name="anndata_out" file="krumsiek11.tl.kmeans.h5ad" ftype="h5ad"/> 322 <output name="anndata_out" file="krumsiek11.tl.kmeans.h5ad" ftype="h5ad"/>
399 </test> 323 </test>
400 <test expect_num_outputs="2"> 324 <test expect_num_outputs="2">
401 <!-- test 5-tl.hc --> 325 <!-- tl.hc -->
402 <param name="adata" value="krumsiek11.pp.lazy.h5ad" /> 326 <param name="adata" value="krumsiek11.pp.lazy.h5ad" />
403 <conditional name="method"> 327 <conditional name="method">
404 <param name="method" value="tl.hc"/> 328 <param name="method" value="tl.hc"/>
405 <param name="hc_num_clusters" value="14"/> 329 <param name="hc_num_clusters" value="14"/>
406 </conditional> 330 </conditional>
417 This function automatically computes PCA coordinates, loadings and variance decomposition, a neighborhood graph of 341 This function automatically computes PCA coordinates, loadings and variance decomposition, a neighborhood graph of
418 observations, t-distributed stochastic neighborhood embedding (tSNE) Uniform Manifold Approximation and Projection (UMAP). 342 observations, t-distributed stochastic neighborhood embedding (tSNE) Uniform Manifold Approximation and Projection (UMAP).
419 343
420 More details on the `episcanpy documentation 344 More details on the `episcanpy documentation
421 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.lazy.html>`__ 345 <https://colomemaria.github.io/episcanpy_doc/api/episcanpy.api.pp.lazy.html>`__
422
423 Find and add gene annotations (`tl.find_genes`)
424 ========================================================================================
425 This function adds a gene annotation to an AnnData (h5ad) file from annotations file (.annotation.gtf).
426 346
427 Automatically obtain target number of clusters (`tl.getNClusters`) 347 Automatically obtain target number of clusters (`tl.getNClusters`)
428 ======================================================================================== 348 ========================================================================================
429 This function will test different settings of louvain to obtain the target number of clusters. 349 This function will test different settings of louvain to obtain the target number of clusters.
430 350