Mercurial > repos > iuc > scanpy_inspect
comparison inspect.xml @ 7:6c145a6868cc draft
"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 |
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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"> |