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comparison inspect.xml @ 7:6c145a6868cc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c"
author iuc
date Wed, 20 May 2020 16:10:30 -0400
parents 5e9171dc8244
children 9d33775ec67d
comparison
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6:5e9171dc8244 7:6c145a6868cc
39 <option value="l2">l2</option> 39 <option value="l2">l2</option>
40 <option value="customized">customized</option> 40 <option value="customized">customized</option>
41 </param> 41 </param>
42 </xml> 42 </xml>
43 <xml name="custom_penalty"> 43 <xml name="custom_penalty">
44 <param argument="pen" type="text" value="" label="Norm used in the penalization" help=""/> 44 <param argument="pen" type="text" value="" label="Norm used in the penalization" help="">
45 <expand macro="sanitize_query" />
46 </param>
45 </xml> 47 </xml>
46 <xml name="random_state"> 48 <xml name="random_state">
47 <param argument="random_state" type="integer" value="" optional="true" 49 <param argument="random_state" type="integer" value="" optional="true"
48 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/> 50 label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>
49 </xml> 51 </xml>
264 <option value="pp.log1p">Logarithmize the data matrix, using 'pp.log1p'</option> 266 <option value="pp.log1p">Logarithmize the data matrix, using 'pp.log1p'</option>
265 <option value="pp.scale">Scale data to unit variance and zero mean, using 'pp.scale'</option> 267 <option value="pp.scale">Scale data to unit variance and zero mean, using 'pp.scale'</option>
266 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option> 268 <option value="pp.sqrt">Square root the data matrix, using 'pp.sqrt'</option>
267 </param> 269 </param>
268 <when value="pp.calculate_qc_metrics"> 270 <when value="pp.calculate_qc_metrics">
269 <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X"/> 271 <param argument="expr_type" type="text" value="counts" label="Name of kind of values in X">
270 <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are"/> 272 <expand macro="sanitize_query" />
271 <param argument="qc_vars" type="text" value="" label="Keys for boolean columns of '.var' which identify variables you could want to control for" 273 </param>
272 help="Keys separated by a comma"/> 274 <param argument="var_type" type="text" value="genes" label="The kind of thing the variables are">
275 <expand macro="sanitize_query" />
276 </param>
277 <param argument="qc_vars" type="text" value="" label="Keys for boolean columns of '.var' which identify variables you could want to control for" help="Keys separated by a comma">
278 <expand macro="sanitize_query" />
279 </param>
273 <param argument="percent_top" type="text" value="" label="Proportions of top genes to cover" 280 <param argument="percent_top" type="text" value="" label="Proportions of top genes to cover"
274 help=" Values (integers) are considered 1-indexed, '50' finds cumulative proportion to the 50th most expressed genes. Values separated by a comma. 281 help=" Values (integers) are considered 1-indexed, '50' finds cumulative proportion to the 50th most expressed genes. Values separated by a comma. If empty don't calculate">
275 If empty don't calculate"/> 282 <expand macro="sanitize_vectors" />
283 </param>
276 </when> 284 </when>
277 <when value="pp.neighbors"> 285 <when value="pp.neighbors">
278 <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If 'knn' is 'True', number of nearest neighbors to be searched. If 'knn' is 'False', a Gaussian kernel width is set to the distance of the 'n_neighbors' neighbor."/> 286 <param argument="n_neighbors" type="integer" min="0" value="15" label="The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation" help="Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100. If 'knn' is 'True', number of nearest neighbors to be searched. If 'knn' is 'False', a Gaussian kernel width is set to the distance of the 'n_neighbors' neighbor."/>
279 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/> 287 <param argument="n_pcs" type="integer" min="0" value="" optional="true" label="Number of PCs to use" help=""/>
280 <param argument="use_rep" type="text" value="" optional="true" label="Indicated representation to use" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter"/> 288 <param argument="use_rep" type="text" value="" optional="true" label="Indicated representation to use" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
289 <expand macro="sanitize_query" />
290 </param>
281 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the 'n_neighbors' nearest neighbor."/> 291 <param argument="knn" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Use a hard threshold to restrict the number of neighbors to n_neighbors?" help="If true, it considers a knn graph. Otherwise, it uses a Gaussian Kernel to assign low weights to neighbors more distant than the 'n_neighbors' nearest neighbor."/>
282 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/> 292 <param argument="random_state" type="integer" value="0" label="Numpy random seed" help=""/>
283 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help=""> 293 <param name="pp_neighbors_method" argument="method" type="select" label="Method for computing connectivities" help="">
284 <option value="umap">umap (McInnes et al, 2018)</option> 294 <option value="umap">umap (McInnes et al, 2018)</option>
285 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option> 295 <option value="gauss">gauss: Gauss kernel following (Coifman et al 2005) with adaptive width (Haghverdi et al 2016)</option>
287 <param argument="metric" type="select" label="Distance metric" help=""> 297 <param argument="metric" type="select" label="Distance metric" help="">
288 <expand macro="distance_metric_options"/> 298 <expand macro="distance_metric_options"/>
289 </param> 299 </param>
290 </when> 300 </when>
291 <when value="tl.score_genes"> 301 <when value="tl.score_genes">
292 <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma"/> 302 <param argument="gene_list" type="text" value="" label="The list of gene names used for score calculation" help="Genes separated by a comma">
303 <expand macro="sanitize_query" />
304 </param>
293 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled" 305 <param argument="ctrl_size" type="integer" value="50" label="Number of reference genes to be sampled"
294 help="If 'len(gene_list)' is not too low, you can set 'ctrl_size=len(gene_list)'."/> 306 help="If 'len(gene_list)' is not too low, you can set 'ctrl_size=len(gene_list)'."/>
295 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set" 307 <param argument="gene_pool" type="text" value="" optional="true" label="Genes for sampling the reference set"
296 help="Default is all genes. Genes separated by a comma"/> 308 help="Default is all genes. Genes separated by a comma">
309 <expand macro="sanitize_query" />
310 </param>
297 <expand macro="score_genes_params"/> 311 <expand macro="score_genes_params"/>
298 <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'" help=""/> 312 <param argument="score_name" type="text" value="score" label="Name of the field to be added in '.obs'" help="">
313 <expand macro="sanitize_query" />
314 </param>
299 </when> 315 </when>
300 <when value="tl.score_genes_cell_cycle"> 316 <when value="tl.score_genes_cell_cycle">
301 <conditional name='s_genes'> 317 <conditional name='s_genes'>
302 <param name="format" type="select" label="Format for the list of genes associated with S phase"> 318 <param name="format" type="select" label="Format for the list of genes associated with S phase">
303 <option value="file">File</option> 319 <option value="file">File</option>
304 <option value="text" selected="true">Text</option> 320 <option value="text" selected="true">Text</option>
305 </param> 321 </param>
306 <when value="text"> 322 <when value="text">
307 <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma"/> 323 <param name="text" type="text" value="" label="List of genes associated with S phase" help="Genes separated by a comma">
324 <expand macro="sanitize_query" />
325 </param>
308 </when> 326 </when>
309 <when value="file"> 327 <when value="file">
310 <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/> 328 <param name="file" type="data" format="txt" label="File with the list of genes associated with S phase" help="One gene per line"/>
311 </when> 329 </when>
312 </conditional> 330 </conditional>
314 <param name="format" type="select" label="Format for the list of genes associated with G2M phase"> 332 <param name="format" type="select" label="Format for the list of genes associated with G2M phase">
315 <option value="file">File</option> 333 <option value="file">File</option>
316 <option value="text" selected="true">Text</option> 334 <option value="text" selected="true">Text</option>
317 </param> 335 </param>
318 <when value="text"> 336 <when value="text">
319 <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma"/> 337 <param name="text" type="text" value="" label="List of genes associated with G2M phase" help="Genes separated by a comma">
338 <expand macro="sanitize_query" />
339 </param>
320 </when> 340 </when>
321 <when value="file"> 341 <when value="file">
322 <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/> 342 <param name="file" type="data" format="txt" label="File with the list of genes associated with G2M phase" help="One gene per line"/>
323 </when> 343 </when>
324 </conditional> 344 </conditional>
325 <expand macro="score_genes_params"/> 345 <expand macro="score_genes_params"/>
326 </when> 346 </when>
327 <when value="tl.rank_genes_groups"> 347 <when value="tl.rank_genes_groups">
328 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help=""/> 348 <param argument="groupby" type="text" value="" label="The key of the observations grouping to consider" help="">
349 <expand macro="sanitize_query" />
350 </param>
329 <expand macro="param_use_raw"/> 351 <expand macro="param_use_raw"/>
330 <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. ['g1', 'g2', 'g3']. If not passed, a ranking will be generated for all groups."/> 352 <param argument="groups" type="text" value="" label="Subset of groups to which comparison shall be restricted" help="e.g. ['g1', 'g2', 'g3']. If not passed, a ranking will be generated for all groups.">
353 <expand macro="sanitize_query" />
354 </param>
331 <conditional name="ref"> 355 <conditional name="ref">
332 <param name="rest" type="select" label="Comparison"> 356 <param name="rest" type="select" label="Comparison">
333 <option value="rest">Compare each group to the union of the rest of the group</option> 357 <option value="rest">Compare each group to the union of the rest of the group</option>
334 <option value="group_id">Compare with respect to a specific group</option> 358 <option value="group_id">Compare with respect to a specific group</option>
335 </param> 359 </param>
336 <when value="rest"/> 360 <when value="rest"/>
337 <when value="group_id"> 361 <when value="group_id">
338 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare"/> 362 <param argument="reference" type="text" value="" label="Group identifier with respect to which compare">
363 <expand macro="sanitize_query" />
364 </param>
339 </when> 365 </when>
340 </conditional> 366 </conditional>
341 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/> 367 <param argument="n_genes" type="integer" min="0" value="100" label="The number of genes that appear in the returned tables" help=""/>
342 <conditional name="tl_rank_genes_groups_method"> 368 <conditional name="tl_rank_genes_groups_method">
343 <param argument="method" type="select" label="Method"> 369 <param argument="method" type="select" label="Method">