Mercurial > repos > bgruening > sklearn_numeric_clustering

comparison numeric_clustering.xml @ 29:c156b85a6389 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
author bgruening
date Sun, 30 Dec 2018 01:39:27 -0500
parents a62c8c1f2ef7
children 60d80322e1e9
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28:2c6c3af5a3cf 29:c156b85a6389
33 my_class = getattr(sklearn.cluster, selected_algorithm) 33 my_class = getattr(sklearn.cluster, selected_algorithm)
34 cluster_object = my_class() 34 cluster_object = my_class()
35 options = params["input_types"]["algorithm_options"]["options"] 35 options = params["input_types"]["algorithm_options"]["options"]
36 36
37 cluster_object.set_params(**options) 37 cluster_object.set_params(**options)
38 if 'n_jobs' in cluster_object.get_params():
39 cluster_object.set_params( n_jobs=N_JOBS )
38 40
39 #if $input_types.selected_input_type == "sparse": 41 #if $input_types.selected_input_type == "sparse":
40 data_matrix = mmread("$infile") 42 data_matrix = mmread("$infile")
41 #else: 43 #else:
42 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) 44 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
160 <!--param argument="compute_full_tree"--> 162 <!--param argument="compute_full_tree"-->
161 <param argument="linkage" type="select" optional="true" label="Linkage" help=""> 163 <param argument="linkage" type="select" optional="true" label="Linkage" help="">
162 <option value="ward" selected="true">ward</option> 164 <option value="ward" selected="true">ward</option>
163 <option value="complete">complete</option> 165 <option value="complete">complete</option>
164 <option value="average">average</option> 166 <option value="average">average</option>
167 <option value="single">single</option>
165 </param> 168 </param>
166 <!--param argument="pooling_func"--> 169 <!--param argument="pooling_func"-->
167 </section> 170 </section>
168 </when> 171 </when>
169 </conditional> 172 </conditional>
281 <param name="eigen_solver" value="arpack"/> 284 <param name="eigen_solver" value="arpack"/>
282 <param name="n_neighbors" value="12"/> 285 <param name="n_neighbors" value="12"/>
283 <param name="n_clusters" value="4"/> 286 <param name="n_clusters" value="4"/>
284 <param name="assign_labels" value="discretize"/> 287 <param name="assign_labels" value="discretize"/>
285 <param name="random_state" value="100"/> 288 <param name="random_state" value="100"/>
286 <output name="outfile" file="cluster_result12" compare="sim_size" /> 289 <output name="outfile" file="cluster_result12.txt" compare="sim_size" />
287 </test> 290 </test>
288 <test> 291 <test>
289 <param name="infile" value="numeric_values.tabular" ftype="tabular"/> 292 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
290 <param name="selected_algorithm" value="SpectralClustering"/> 293 <param name="selected_algorithm" value="SpectralClustering"/>
291 <param name="selected_input_type" value="tabular"/> 294 <param name="selected_input_type" value="tabular"/>