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comparison inspect.xml @ 1:05304c5c195d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:27:55 -0400
parents b2a6ce371781
children 70f5f1fee692
comparison
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0:b2a6ce371781 1:05304c5c195d
9 @CMD@ 9 @CMD@
10 ]]></command> 10 ]]></command>
11 <configfiles> 11 <configfiles>
12 <configfile name="script_file"><![CDATA[ 12 <configfile name="script_file"><![CDATA[
13 @CMD_imports@ 13 @CMD_imports@
14 import pandas as pd
15 from scipy import io
16
17 pd.options.display.precision = 15
14 18
15 adata = ad.read('$input') 19 adata = ad.read('$input')
16 20
17 #if $inspect.info == 'general' 21 #if $inspect.info == 'general'
18 with open('$general', 'w') as f: 22 with open('$general', 'w') as f:
19 print(adata, file=f) 23 print(adata, file=f)
24
20 #else if $inspect.info == 'X' 25 #else if $inspect.info == 'X'
21 adata.to_df().to_csv('$X', sep='\t') 26 adata.to_df().to_csv('$X', sep='\t')
27
22 #else if $inspect.info == 'obs' 28 #else if $inspect.info == 'obs'
23 adata.obs.to_csv('$obs', sep='\t') 29 adata.obs.to_csv('$obs', sep='\t')
30
24 #else if $inspect.info == 'var' 31 #else if $inspect.info == 'var'
25 adata.var.to_csv('$var', sep='\t') 32 adata.var.to_csv('$var', sep='\t')
33
26 #else if $inspect.info == 'chunk_X' 34 #else if $inspect.info == 'chunk_X'
27 import pandas as pd
28 #if $inspect.chunk.info == 'random' 35 #if $inspect.chunk.info == 'random'
29 X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace) 36 X = adata.chunk_X(select=$inspect.chunk.size, replace=$inspect.chunk.replace)
30 #else 37 #else
31 #set $select = [int(x.strip()) for x in str($inspect.chunk.list).split(',')] 38 #set $select = [int(x.strip()) for x in str($inspect.chunk.list).split(',')]
32 X = adata.chunk_X(select=$select) 39 X = adata.chunk_X(select=$select)
33 #end if 40 #end if
34 pd.DataFrame(X).to_csv('$chunk_X', sep='\t') 41 pd.DataFrame(X).to_csv('$chunk_X', sep='\t')
42
43 #else if $inspect.info == 'uns'
44 #if $inspect.uns_info == 'neighbors'
45 io.mmwrite('uns_neighbors_connectivities.mtx', adata.uns['neighbors']['connectivities'])
46 io.mmwrite('uns_neighbors_distances.mtx', adata.uns['neighbors']['distances'])
47 #else if $inspect.uns_info == 'paga'
48 io.mmwrite('uns_paga_connectivities.mtx', adata.uns['paga']['connectivities'])
49 io.mmwrite('uns_paga_connectivities_tree.mtx', adata.uns['paga']['connectivities_tree'])
50 #else if $inspect.uns_info == 'pca'
51 pd.DataFrame(adata.uns['pca']['variance']).to_csv("$uns_pca_variance", sep="\t", index = False)
52 pd.DataFrame(adata.uns['pca']['variance_ratio']).to_csv("$uns_pca_variance_ratio", sep="\t", index = False)
53 #else if $inspect.uns_info == 'rank_genes_groups'
54 pd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges']).to_csv("$uns_rank_genes_groups_logfoldchanges", sep="\t", index = False)
55 pd.DataFrame(adata.uns['rank_genes_groups']['names']).to_csv("$uns_rank_genes_groups_names", sep="\t", index = False)
56 pd.DataFrame(adata.uns['rank_genes_groups']['pvals']).to_csv("$uns_rank_genes_groups_pvals", sep="\t", index = False)
57 pd.DataFrame(adata.uns['rank_genes_groups']['pvals_adj']).to_csv("$uns_rank_genes_groups_pvals_adj", sep="\t", index = False)
58 pd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv("$uns_rank_genes_groups_scores", sep="\t", index = False)
59 #end if
60
61 #else if $inspect.info == 'obsm'
62 #if $inspect.obsm_info == 'X_pca'
63 pd.DataFrame(adata.obsm['X_pca']).to_csv("$obsm_X_pca", sep="\t", index = False)
64 #else if $inspect.obsm_info == 'X_umap'
65 pd.DataFrame(adata.obsm['X_umap']).to_csv("$obsm_X_umap", sep="\t", index = False)
66 #else if $inspect.obsm_info == 'X_tsne'
67 pd.DataFrame(adata.obsm['X_tsne']).to_csv("$obsm_X_tsne", sep="\t", index = False)
68 #else if $inspect.obsm_info == 'X_draw_graph'
69 for key in adata.obsm.keys():
70 if key.startswith('X_draw_graph'):
71 pd.DataFrame(adata.obsm[key]).to_csv(key, sep="\t", index = False)
72 #else if $inspect.obsm_info == 'X_diffmap'
73 pd.DataFrame(adata.obsm['X_diffmap']).to_csv("$obsm_X_diffmap", sep="\t", index = False)
74 #end if
75
76 #else if $inspect.info == 'varm'
77 #if $inspect.varm_info == 'PCs'
78 pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False)
79 #end if
80
35 #end if 81 #end if
36 ]]></configfile> 82 ]]></configfile>
37 </configfiles> 83 </configfiles>
38 <inputs> 84 <inputs>
39 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/> 85 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
40 <conditional name="inspect"> 86 <conditional name="inspect">
41 <param name="info" type="select" label="What to inspect?"> 87 <param name="info" type="select" label="What to inspect?">
42 <option value="general">General information about the object</option> 88 <option value="general">General information about the object</option>
43 <option value="X">The full data matrix</option> 89 <option value="X">The full data matrix</option>
44 <option value="chunk_X">A chunk of the data matrix</option> 90 <option value="chunk_X">A chunk of the data matrix</option>
45 <option value="obs">Key-indexed observations annotation</option> 91 <option value="obs">Key-indexed observations annotation (obs)</option>
46 <option value="var">Key-indexed annotation of variables/features</option> 92 <option value="var">Key-indexed annotation of variables/features (var)</option>
47 <!--<option value="uns">Unstructured annotation</option>!--> 93 <option value="uns">Unstructured annotation (uns)</option>
94 <option value="obsm">Multi-dimensional observations annotation (obsm)</option>
95 <option value="varm">Multi-dimensional variables annotation (varm)</option>
48 </param> 96 </param>
49 <when value="general"/> 97 <when value="general"/>
50 <when value="X"/> 98 <when value="X"/>
99 <when value="chunk_X">
100 <expand macro="params_chunk_X"/>
101 </when>
51 <when value="obs"/> 102 <when value="obs"/>
52 <when value="var"/> 103 <when value="var"/>
53 <when value="chunk_X"> 104 <when value="uns">
54 <expand macro="params_chunk_X"/> 105 <param name="uns_info" type="select" label="What to inspect in uns?">
106 <option value="neighbors">Neighbors</option>
107 <option value="paga">PAGA</option>
108 <option value="pca">PCA</option>
109 <option value="rank_genes_groups">Rank gene groups (rank_genes_groups)</option>
110 </param>
111 </when>
112 <when value="obsm">
113 <param name="obsm_info" type="select" label="Which annotation to inspect for the observations?">
114 <option value="X_pca">PCA coordinates (X_pca)</option>
115 <option value="X_umap">UMAP coordinates (X_umap)</option>
116 <option value="X_tsne">tSNE coordinates (X_tsne)</option>
117 <option value="X_draw_graph">Coordinates of graph layout (X_draw_graph)</option>
118 <option value="X_diffmap">Diffusion map representation of data (X_diffmap)</option>
119 </param>
120 </when>
121 <when value="varm">
122 <param name="varm_info" type="select" label="Which annotation to inspect for the variables?">
123 <option value="PCs">Principal components containing the loadings</option>
124 </param>
55 </when> 125 </when>
56 </conditional> 126 </conditional>
57 </inputs> 127 </inputs>
58 <outputs> 128 <outputs>
59 <data name="general" format="txt" label="${tool.name} on ${on_string}: General information"> 129 <data name="general" format="txt" label="${tool.name} on ${on_string}: General information">
69 <filter>inspect['info'] == 'var'</filter> 139 <filter>inspect['info'] == 'var'</filter>
70 </data> 140 </data>
71 <data name="chunk_X" format="tabular" label="${tool.name} on ${on_string}: Observations annotation"> 141 <data name="chunk_X" format="tabular" label="${tool.name} on ${on_string}: Observations annotation">
72 <filter>inspect['info'] == 'chunk_X'</filter> 142 <filter>inspect['info'] == 'chunk_X'</filter>
73 </data> 143 </data>
144 <data name="uns_neighbors_connectivities" format="mtx" from_work_dir="uns_neighbors_connectivities.mtx" label="${tool.name} on ${on_string}: Weighted adjacency matrix of the neighborhood graph of data points">
145 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'neighbors'</filter>
146 </data>
147 <data name="uns_neighbors_distances" format="mtx" from_work_dir="uns_neighbors_distances.mtx" label="${tool.name} on ${on_string}: Distances for each pair of neighbors">
148 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'neighbors'</filter>
149 </data>
150 <data name="uns_paga_connectivities" format="mtx" from_work_dir="uns_paga_connectivities.mtx" label="${tool.name} on ${on_string}: Full adjacency matrix of the abstracted graph">
151 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'paga'</filter>
152 </data>
153 <data name="uns_paga_connectivities_tree" format="mtx" from_work_dir="uns_paga_connectivities_tree.mtx" label="${tool.name} on ${on_string}: Adjacency matrix of the tree-like subgraph">
154 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'paga'</filter>
155 </data>
156 <data name="uns_pca_variance" format="tabular" label="${tool.name} on ${on_string}: Ratio of explained variance for PCA">
157 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'pca'</filter>
158 </data>
159 <data name="uns_pca_variance_ratio" format="tabular" label="${tool.name} on ${on_string}: Explained variance, equivalent to the eigenvalues of the covariance matrix, for PCA">
160 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'pca'</filter>
161 </data>
162 <data name="uns_rank_genes_groups_names" format="tabular" label="${tool.name} on ${on_string}: Names for rank genes">
163 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'rank_genes_groups'</filter>
164 </data>
165 <data name="uns_rank_genes_groups_scores" format="tabular" label="${tool.name} on ${on_string}: Z-scores for rank genes">
166 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'rank_genes_groups'</filter>
167 </data>
168 <data name="uns_rank_genes_groups_logfoldchanges" format="tabular" label="${tool.name} on ${on_string}: Log2 fold changes for rank genes">
169 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'rank_genes_groups'</filter>
170 </data>
171 <data name="uns_rank_genes_groups_pvals" format="tabular" label="${tool.name} on ${on_string}: P-values for rank genes">
172 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'rank_genes_groups'</filter>
173 </data>
174 <data name="uns_rank_genes_groups_pvals_adj" format="tabular" label="${tool.name} on ${on_string}: Adjusted p-values for rank genes">
175 <filter>inspect['info'] == 'uns' and inspect['uns_info'] == 'rank_genes_groups'</filter>
176 </data>
177 <data name="obsm_X_pca" format="tabular" label="${tool.name} on ${on_string}: PCA coordinates for observations">
178 <filter>inspect['info'] == 'obsm' and inspect['obsm_info'] == 'X_pca'</filter>
179 </data>
180 <data name="obsm_X_umap" format="tabular" label="${tool.name} on ${on_string}: UMAP coordinates for observations">
181 <filter>inspect['info'] == 'obsm' and inspect['obsm_info'] == 'X_umap'</filter>
182 </data>
183 <data name="obsm_X_tsne" format="tabular" label="${tool.name} on ${on_string}: tSNE coordinates for observations">
184 <filter>inspect['info'] == 'obsm' and inspect['obsm_info'] == 'X_tsne'</filter>
185 </data>
186 <collection name="obsm_X_draw_graph" type="list" label="${tool.name} on ${on_string}: Coordinates of graph layout">
187 <discover_datasets pattern="X_draw_graph_(?P&lt;designation&gt;.*)" format="tabular"/>
188 <filter>inspect['info'] == 'obsm' and inspect['obsm_info'] == 'X_draw_graph'</filter>
189 </collection>
190 <data name="obsm_X_diffmap" format="tabular" label="${tool.name} on ${on_string}: Diffusion map representation for observations">
191 <filter>inspect['info'] == 'obsm' and inspect['obsm_info'] == 'X_diffmap'</filter>
192 </data>
193 <data name="varm_PCs" format="tabular" label="${tool.name} on ${on_string}: Principal components containing the loadings for variables">
194 <filter>inspect['info'] == 'varm' and inspect['varm_info'] == 'PCs'</filter>
195 </data>
74 </outputs> 196 </outputs>
75 <tests> 197 <tests>
76 <test> 198 <test>
199 <!-- test 1: general info -->
77 <param name="input" value="krumsiek11.h5ad"/> 200 <param name="input" value="krumsiek11.h5ad"/>
78 <conditional name="inspect"> 201 <conditional name="inspect">
79 <param name="info" value="general"/> 202 <param name="info" value="general"/>
80 </conditional> 203 </conditional>
81 <output name="general" value="inspect.general.txt"/> 204 <output name="general" value="inspect.general.txt"/>
82 </test> 205 </test>
83 <test> 206 <test>
207 <!-- test 2: X -->
84 <param name="input" value="krumsiek11.h5ad"/> 208 <param name="input" value="krumsiek11.h5ad"/>
85 <conditional name="inspect"> 209 <conditional name="inspect">
86 <param name="info" value="X"/> 210 <param name="info" value="X"/>
87 </conditional> 211 </conditional>
88 <assert_stdout> 212 <assert_stdout>
89 <has_text_matching expression="adata.to_df\(\).to_csv"/> 213 <has_text_matching expression="adata.to_df\(\).to_csv"/>
90 </assert_stdout> 214 </assert_stdout>
91 <output name="X" value="inspect.X.tabular" ftype="tabular"/> 215 <output name="X" value="inspect.X.tabular" ftype="tabular"/>
92 </test> 216 </test>
93 <test> 217 <test>
218 <!-- test 3: obs -->
94 <param name="input" value="krumsiek11.h5ad"/> 219 <param name="input" value="krumsiek11.h5ad"/>
95 <conditional name="inspect"> 220 <conditional name="inspect">
96 <param name="info" value="obs"/> 221 <param name="info" value="obs"/>
97 </conditional> 222 </conditional>
98 <assert_stdout> 223 <assert_stdout>
99 <has_text_matching expression="adata.obs.to_csv"/> 224 <has_text_matching expression="adata.obs.to_csv"/>
100 </assert_stdout> 225 </assert_stdout>
101 <output name="obs" value="inspect.obs.tabular" ftype="tabular"/> 226 <output name="obs" value="inspect.obs.tabular" ftype="tabular"/>
102 </test> 227 </test>
103 <test> 228 <test>
229 <!-- test 4: var -->
104 <param name="input" value="krumsiek11.h5ad"/> 230 <param name="input" value="krumsiek11.h5ad"/>
105 <conditional name="inspect"> 231 <conditional name="inspect">
106 <param name="info" value="var"/> 232 <param name="info" value="var"/>
107 </conditional> 233 </conditional>
108 <assert_stdout> 234 <assert_stdout>
109 <has_text_matching expression="adata.var.to_csv"/> 235 <has_text_matching expression="adata.var.to_csv"/>
110 </assert_stdout> 236 </assert_stdout>
111 <output name="var" value="inspect.var.tabular" ftype="tabular"/> 237 <output name="var" value="inspect.var.tabular" ftype="tabular"/>
112 </test> 238 </test>
113 <test> 239 <test>
240 <!-- test 5: chunk_X, specified -->
114 <param name="input" value="krumsiek11.h5ad"/> 241 <param name="input" value="krumsiek11.h5ad"/>
115 <conditional name="inspect"> 242 <conditional name="inspect">
116 <param name="info" value="chunk_X"/> 243 <param name="info" value="chunk_X"/>
117 <conditional name="chunk"> 244 <conditional name="chunk">
118 <param name="info" value="specified"/> 245 <param name="info" value="specified"/>
124 <has_text_matching expression="select=\[3, 5, 8\]"/> 251 <has_text_matching expression="select=\[3, 5, 8\]"/>
125 </assert_stdout> 252 </assert_stdout>
126 <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/> 253 <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/>
127 </test> 254 </test>
128 <test> 255 <test>
256 <!-- test 6: chunk_X, random -->
129 <param name="input" value="krumsiek11.h5ad"/> 257 <param name="input" value="krumsiek11.h5ad"/>
130 <conditional name="inspect"> 258 <conditional name="inspect">
131 <param name="info" value="chunk_X"/> 259 <param name="info" value="chunk_X"/>
132 <conditional name="chunk"> 260 <conditional name="chunk">
133 <param name="info" value="random"/> 261 <param name="info" value="random"/>
144 <assert_contents> 272 <assert_contents>
145 <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/> 273 <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/>
146 </assert_contents> 274 </assert_contents>
147 </output> 275 </output>
148 </test> 276 </test>
277 <test>
278 <!-- test 7: uns, neighbors -->
279 <param name="input" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
280 <conditional name="inspect">
281 <param name="info" value="uns"/>
282 <param name="uns_info" value="neighbors"/>
283 </conditional>
284 <output name="uns_neighbors_connectivities" ftype="mtx">
285 <assert_contents>
286 <has_text_matching expression="100 100 1248" />
287 <has_text_matching expression="4.880" />
288 </assert_contents>
289 </output>
290 <output name="uns_neighbors_distances" ftype="mtx">
291 <assert_contents>
292 <has_text_matching expression="100 100 1400" />
293 <has_text_matching expression="4.973" />
294 <has_text_matching expression="4.877" />
295 </assert_contents>
296 </output>
297 </test>
298 <test>
299 <!-- test 8: uns, paga -->
300 <param name="input" value="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
301 <conditional name="inspect">
302 <param name="info" value="uns"/>
303 <param name="uns_info" value="paga"/>
304 </conditional>
305 <output name="uns_paga_connectivities" ftype="mtx">
306 <assert_contents>
307 <has_text_matching expression="16 16 97" />
308 <has_text_matching expression="1.000" />
309 <has_text_matching expression="8.839" />
310 </assert_contents>
311 </output>
312 <output name="uns_paga_connectivities_tree" ftype="mtx">
313 <assert_contents>
314 <has_text_matching expression="16 16 15" />
315 <has_text_matching expression="1.000" />
316 </assert_contents>
317 </output>
318 </test>
319 <test>
320 <!-- test 9: uns, pca -->
321 <param name="input" value="pp.pca.krumsiek11.h5ad"/>
322 <conditional name="inspect">
323 <param name="info" value="uns"/>
324 <param name="uns_info" value="pca"/>
325 </conditional>
326 <output name="uns_pca_variance">
327 <assert_contents>
328 <has_text_matching expression="0.75409454" />
329 <has_text_matching expression="3.2818672e-05" />
330 <has_n_columns n="1" />
331 </assert_contents>
332 </output>
333 <output name="uns_pca_variance_ratio">
334 <assert_contents>
335 <has_text_matching expression="0.039053127" />
336 <has_text_matching expression="0.00013167" />
337 <has_n_columns n="1" />
338 </assert_contents>
339 </output>
340 </test>
341 <test>
342 <!-- test 10: uns, rank_gene_groups -->
343 <param name="input" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
344 <conditional name="inspect">
345 <param name="info" value="uns"/>
346 <param name="uns_info" value="rank_genes_groups"/>
347 </conditional>
348 <output name="uns_rank_genes_groups_names">
349 <assert_contents>
350 <has_n_columns n="5" />
351 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
352 <has_text_matching expression="Gata1\tFog1\tCebpa\tFli1\tGata2"/>
353 <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/>
354 </assert_contents>
355 </output>
356 <output name="uns_rank_genes_groups_scores">
357 <assert_contents>
358 <has_n_columns n="5" />
359 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/>
360 <has_text_matching expression="18.86\d{4}"/>
361 <has_text_matching expression="17.85\d{4}"/>
362 <has_text_matching expression="-2.63\d{4}"/>
363 <has_text_matching expression="-2.98\d{4}"/>
364 <has_text_matching expression="-6.41\d{4}"/>
365 </assert_contents>
366 </output>
367 <output name="uns_rank_genes_groups_logfoldchanges">
368 <assert_contents>
369 <has_n_columns n="5" />
370 </assert_contents>
371 </output>
372 <output name="uns_rank_genes_groups_pvals">
373 <assert_contents>
374 <has_n_columns n="5" />
375 <has_text_matching expression="1.8000"/>
376 </assert_contents>
377 </output>
378 <output name="uns_rank_genes_groups_pvals_adj">
379 <assert_contents>
380 <has_n_columns n="5" />
381 <has_text_matching expression="1.98004"/>
382 </assert_contents>
383 </output>
384 </test>
385 <test>
386 <!-- test 11: obsm, X_pca -->
387 <param name="input" value="pp.pca.krumsiek11.h5ad"/>
388 <conditional name="inspect">
389 <param name="info" value="obsm"/>
390 <param name="obsm_info" value="X_pca"/>
391 </conditional>
392 <output name="obsm_X_pca">
393 <assert_contents>
394 <has_text_matching expression="0.00030471283" />
395 <has_text_matching expression="3.4109413e-05" />
396 <has_text_matching expression="-0.6401007" />
397 <has_n_columns n="10" />
398 </assert_contents>
399 </output>
400 </test>
401 <test>
402 <!-- test 12: obsm_info, X_umap -->
403 <param name="input" value="tl.umap.h5ad"/>
404 <conditional name="inspect">
405 <param name="info" value="obsm"/>
406 <param name="obsm_info" value="X_umap"/>
407 </conditional>
408 <output name="obsm_X_umap">
409 <assert_contents>
410 <has_text text="1.664" />
411 <has_text text="5.425" />
412 <has_text text="-1.748" />
413 <has_text text="-9.714" />
414 <has_n_columns n="2" />
415 </assert_contents>
416 </output>
417 </test>
418 <test>
419 <!-- test 13: obsm_info, X_tsne -->
420 <param name="input" value="tl.tsne.h5ad"/>
421 <conditional name="inspect">
422 <param name="info" value="obsm"/>
423 <param name="obsm_info" value="X_tsne"/>
424 </conditional>
425 <output name="obsm_X_tsne">
426 <assert_contents>
427 <has_text text="14.301989" />
428 <has_text text="-19.447426" />
429 <has_n_columns n="2" />
430 </assert_contents>
431 </output>
432 </test>
433 <test>
434 <!-- test 14: obsm_info, X_draw_graph -->
435 <param name="input" value="tl.draw_graph.h5ad"/>
436 <conditional name="inspect">
437 <param name="info" value="obsm"/>
438 <param name="obsm_info" value="X_draw_graph"/>
439 </conditional>
440 <output_collection name="obsm_X_draw_graph">
441 <element name="fr">
442 <assert_contents>
443 <has_text text="-39.77" />
444 <has_text text="-24.83" />
445 <has_text text="-34.34" />
446 <has_text text="-22.34" />
447 <has_n_columns n="2" />
448 </assert_contents>
449 </element>
450 </output_collection>
451 </test>
452 <test>
453 <!-- test 15: obsm_info, X_diffmap -->
454 <param name="input" value="tl.diffmap.h5ad"/>
455 <conditional name="inspect">
456 <param name="info" value="obsm"/>
457 <param name="obsm_info" value="X_diffmap"/>
458 </conditional>
459 <output name="obsm_X_diffmap">
460 <assert_contents>
461 <has_text text="0.1006" />
462 <has_text text="-0.0619" />
463 <has_n_columns n="15" />
464 </assert_contents>
465 </output>
466 </test>
467 <test>
468 <!-- test 16: varm_info, PCs -->
469 <param name="input" value="pp.pca.krumsiek11.h5ad"/>
470 <conditional name="inspect">
471 <param name="info" value="varm"/>
472 <param name="varm_info" value="PCs"/>
473 </conditional>
474 <output name="varm_PCs">
475 <assert_contents>
476 <has_text_matching expression="0.2352" />
477 <has_text_matching expression="-0.0492" />
478 <has_n_columns n="10" />
479 </assert_contents>
480 </output>
481 </test>
149 </tests> 482 </tests>
150 <help><![CDATA[ 483 <help><![CDATA[
151 **What it does** 484 **What it does**
152 485
153 This tool inspects a AnnData dataset and returns: 486 This tool inspects a AnnData dataset and returns: