Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison cluster_reduce_dimension.xml @ 7:aab193557a1d 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 12:20:33 +0000
parents bd6d678d0579
children f74735a64736
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6:bd6d678d0579 7:aab193557a1d
2 <description>with scanpy</description> 2 <description>with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="pca_inputs"> 5 <xml name="pca_inputs">
6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/> 6 <param argument="n_comps" type="integer" min="0" value="50" label="Number of principal components to compute" help=""/>
7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help=""/> 7 <param argument="dtype" type="text" value="float32" label="Numpy data type string to which to convert the result" help="">
8 <expand macro="sanitize_query" />
9 </param>
8 <conditional name="pca"> 10 <conditional name="pca">
9 <param argument="chunked" type="select" label="Type of PCA?"> 11 <param argument="chunked" type="select" label="Type of PCA?">
10 <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of 'random_seed' and 'svd_solver')</option> 12 <option value="True">Incremental PCA on segments (incremental PCA automatically zero centers and ignores settings of 'random_seed' and 'svd_solver')</option>
11 <option value="False" selected="true">Full PCA</option> 13 <option value="False" selected="true">Full PCA</option>
12 </param> 14 </param>
208 help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2009"/> 210 help="Higher resolution means finding more and smaller clusters, which defaults to 1.0. See “Time as a resolution parameter” in Lambiotte et al, 2009"/>
209 </when> 211 </when>
210 <when value="igraph"/> 212 <when value="igraph"/>
211 </conditional> 213 </conditional>
212 <expand macro="param_random_state"/> 214 <expand macro="param_random_state"/>
213 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help=""/> 215 <param argument="key_added" type="text" value="louvain" optional="true" label="Key under which to add the cluster labels" help="">
216 <expand macro="sanitize_query" />
217 </param>
214 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/> 218 <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Interpret the adjacency matrix as directed graph?"/>
215 <expand macro="param_use_weights"/> 219 <expand macro="param_use_weights"/>
216 </when> 220 </when>
217 <when value="tl.leiden"> 221 <when value="tl.leiden">
218 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/> 222 <param argument="resolution" type="float" value="1" label="Coarseness of the clusterin" help="Higher values lead to more clusters"/>
219 <expand macro="param_random_state"/> 223 <expand macro="param_random_state"/>
220 <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help=""/> 224 <param argument="key_added" type="text" value="leiden" label="Key under which to add the cluster labels" help="">
225 <expand macro="sanitize_query" />
226 </param>
221 <expand macro="param_use_weights"/> 227 <expand macro="param_use_weights"/>
222 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/> 228 <param argument="n_iterations" type="integer" value="-1" label="How many iterations of the Leiden clustering algorithm to perform." help="Positive values above 2 define the total number of iterations to perform, -1 has the algorithm run until it reaches its optimal clustering."/>
223 </when> 229 </when>
224 <when value="pp.pca"> 230 <when value="pp.pca">
225 <expand macro="pca_inputs"/> 231 <expand macro="pca_inputs"/>
255 </when> 261 </when>
256 <when value="tl.draw_graph"> 262 <when value="tl.draw_graph">
257 <expand macro="param_layout"/> 263 <expand macro="param_layout"/>
258 <expand macro="param_root"/> 264 <expand macro="param_root"/>
259 <expand macro="param_random_state"/> 265 <expand macro="param_random_state"/>
260 <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)"/> 266 <param argument="init_pos" type="text" optional="true" value="" label="Precomputed coordinates for initialization" help="It should be a valid 2d observation (e.g. paga)">
267 <expand macro="sanitize_query" />
268 </param>
261 <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/> 269 <param argument="adjacency" type="data" format="mtx" optional="true" label="Sparse adjacency matrix of the graph" help="If not set, it uses the unstructured annotation (uns) / neighbors / connectivities"/>
262 <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'"/> 270 <param argument="key_ext" type="text" optional="true" value="" label="External key" help="If not set, it appends 'layout'">
271 <expand macro="sanitize_query" />
272 </param>
263 </when> 273 </when>
264 <when value="tl.dpt"> 274 <when value="tl.dpt">
265 <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/> 275 <param argument="n_dcs" type="integer" min="0" value="10" label="Number of diffusion components to use" help=""/>
266 <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect" help=""/> 276 <param argument="n_branchings" type="integer" min="0" value="0" label="Number of branchings to detect" help=""/>
267 <param argument="min_group_size" type="float" min="0" value="0.01" label="Min group size" help="During recursive splitting of branches ('dpt groups') for 'n_branchings' &gt; 1, do not consider groups that contain less than 'min_group_size' data points. If a float, 'min_group_size' refers to a fraction of the total number of data points."/> 277 <param argument="min_group_size" type="float" min="0" value="0.01" label="Min group size" help="During recursive splitting of branches ('dpt groups') for 'n_branchings' &gt; 1, do not consider groups that contain less than 'min_group_size' data points. If a float, 'min_group_size' refers to a fraction of the total number of data points."/>
268 <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/> 278 <param argument="allow_kendall_tau_shift" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Allow Kendal tau shift?" help="If a very small branch is detected upon splitting, shift away from maximum correlation in Kendall tau criterion of Haghverdi et al (2016) to stabilize the splitting."/>
269 </when> 279 </when>
270 <when value="tl.paga"> 280 <when value="tl.paga">
271 <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs')."/> 281 <param argument="groups" type="text" value="louvain" label="Key for categorical in the input" help="You can pass your predefined groups by choosing any categorical annotation of observations ('adata.obs').">
282 <expand macro="sanitize_query" />
283 </param>
272 <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/> 284 <param argument="use_rna_velocity" type="boolean" truevalue="False" falsevalue="False" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions?" help="Requires that 'adata.uns' contains a directed single-cell graph with key '['velocyto_transitions']'. This feature might be subject to change in the future."/>
273 <param argument="model" type="select" label="PAGA connectivity model" help=""> 285 <param argument="model" type="select" label="PAGA connectivity model" help="">
274 <option value="v1.2">v1.2</option> 286 <option value="v1.2">v1.2</option>
275 <option value="v1.0">v1.0</option> 287 <option value="v1.0">v1.0</option>
276 </param> 288 </param>