Repository 'sklearn_generalized_linear'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear

Changeset 16:8ccc9b001a88 (2018-08-04)
Previous changeset 15:f0e215cbade3 (2018-07-13) Next changeset 17:3b72ac38dfff (2018-08-04)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
modified:
main_macros.xml
test-data/feature_selection_result01
test-data/feature_selection_result08
test-data/feature_selection_result09
added:
test-data/feature_selection_result12
test-data/pipeline01
test-data/pipeline02
test-data/pipeline03
test-data/pipeline04
test-data/pipeline05
test-data/pipeline06
test-data/pipeline07
test-data/pipeline08
test-data/searchCV01
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diff -r f0e215cbade3 -r 8ccc9b001a88 main_macros.xml
--- a/main_macros.xml Fri Jul 13 03:56:33 2018 -0400
+++ b/main_macros.xml Sat Aug 04 12:30:07 2018 -0400
[
b'@@ -34,24 +34,20 @@\n   if inputs[\'selected_algorithm\'] == \'SelectFromModel\':\n     if not options[\'threshold\'] or options[\'threshold\'] == \'None\':\n       options[\'threshold\'] = None\n-      if \'extra_estimator\' in inputs and inputs[\'extra_estimator\'][\'has_estimator\'] == \'no_load\':\n-        with open("inputs[\'extra_estimator\'][\'fitted_estimator\']", \'rb\') as model_handler:\n-          fitted_estimator = pickle.load(model_handler)\n-        new_selector = selector(fitted_estimator, prefit=True, **options)\n-      else:\n-        estimator=inputs["estimator"]\n-        if inputs["extra_estimator"]["has_estimator"]==\'no\':\n-          estimator=inputs["extra_estimator"]["new_estimator"]\n-        estimator=eval(estimator.replace(\'__dq__\', \'"\').replace("__sq__","\'"))\n-        new_selector = selector(estimator, **options)\n+    if inputs[\'model_inputter\'][\'input_mode\'] == \'prefitted\':\n+      model_file = inputs[\'model_inputter\'][\'fitted_estimator\']\n+      with open(model_file, \'rb\') as model_handler:\n+        fitted_estimator = pickle.load(model_handler)\n+      new_selector = selector(fitted_estimator, prefit=True, **options)\n+    else:\n+      estimator_json = inputs[\'model_inputter\']["estimator_selector"]\n+      estimator = get_estimator(estimator_json)\n+      new_selector = selector(estimator, **options)\n \n   elif inputs[\'selected_algorithm\'] in [\'RFE\', \'RFECV\']:\n     if \'scoring\' in options and (not options[\'scoring\'] or options[\'scoring\'] == \'None\'):\n       options[\'scoring\'] = None\n-    estimator=inputs["estimator"]\n-    if inputs["extra_estimator"]["has_estimator"]==\'no\':\n-      estimator=inputs["extra_estimator"]["new_estimator"]\n-    estimator=eval(estimator.replace(\'__dq__\', \'"\').replace("__sq__","\'"))\n+    estimator=get_estimator(inputs["estimator_selector"])\n     new_selector = selector(estimator, **options)\n \n   elif inputs[\'selected_algorithm\'] == "VarianceThreshold":\n@@ -104,11 +100,101 @@\n   return X, y\n   </token>\n \n+  <token name="@GET_SEARCH_PARAMS_FUNCTION@">\n+def get_search_params(params_builder):\n+  search_params = {}\n+\n+  def safe_eval(literal):\n+\n+    FROM_SCIPY_STATS = [  \'bernoulli\', \'binom\', \'boltzmann\', \'dlaplace\', \'geom\', \'hypergeom\',\n+                          \'logser\', \'nbinom\', \'planck\', \'poisson\', \'randint\', \'skellam\', \'zipf\' ]\n+\n+    FROM_NUMPY_RANDOM = [ \'beta\', \'binomial\', \'bytes\', \'chisquare\', \'choice\', \'dirichlet\', \'division\',\n+                          \'exponential\', \'f\', \'gamma\', \'geometric\', \'gumbel\', \'hypergeometric\',\n+                          \'laplace\', \'logistic\', \'lognormal\', \'logseries\', \'mtrand\', \'multinomial\',\n+                          \'multivariate_normal\', \'negative_binomial\', \'noncentral_chisquare\', \'noncentral_f\',\n+                          \'normal\', \'pareto\', \'permutation\', \'poisson\', \'power\', \'rand\', \'randint\',\n+                          \'randn\', \'random\', \'random_integers\', \'random_sample\', \'ranf\', \'rayleigh\',\n+                          \'sample\', \'seed\', \'set_state\', \'shuffle\', \'standard_cauchy\', \'standard_exponential\',\n+                          \'standard_gamma\', \'standard_normal\', \'standard_t\', \'triangular\', \'uniform\',\n+                          \'vonmises\', \'wald\', \'weibull\', \'zipf\' ]\n+\n+    # File opening and other unneeded functions could be dropped\n+    UNWANTED = [\'open\', \'type\', \'dir\', \'id\', \'str\', \'repr\']\n+\n+    # Allowed symbol table. Add more if needed.\n+    new_syms = {\n+      \'np_arange\': getattr(np, \'arange\'),\n+      \'ensemble_ExtraTreesClassifier\': getattr(ensemble, \'ExtraTreesClassifier\')\n+    }\n+\n+    syms = make_symbol_table(use_numpy=False, **new_syms)\n+\n+    for method in FROM_SCIPY_STATS:\n+      syms[\'scipy_stats_\' + method] = getattr(scipy.stats, method)\n+\n+    for func in FROM_NUMPY_RANDOM:\n+      syms[\'np_random_\' + func] = getattr(np.random, func)\n+\n+    for key in UNWANTED:\n+      syms.pop(key, None)\n+\n+    aeval = Interpreter(symtable=syms, use_numpy=False, minimal=False,\n+                      no_if=True, no_for=True, no_while=True, no_try=True,\n+                '..b'"Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'whiten\': False. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="KernelPCA">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="LatentDirichletAllocation">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="MiniBatchDictionaryLearning">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="MiniBatchSparsePCA">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="NMF">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'init\': \'random\'. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="PCA">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="SparsePCA">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 100, \'random_state\': 42. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="SparseCoder">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'transform_algorithm\': \'omp\', \'transform_alpha\': 1.0. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+      <when value="TruncatedSVD">\n+        <expand macro="estimator_params_text" label="Type in maxtrix decomposition parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_components\': 2, \'algorithm\': \'randomized\'. No double quotes. Leave this box blank for default estimator."/>\n+      </when>\n+    </conditional>\n+  </xml>\n+\n+  <xml name="FeatureAgglomeration">\n+    <conditional name="FeatureAgglomeration_selector">\n+      <param name="select_algorithm" type="select" label="Choose the algorithm:">\n+        <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option>\n+      </param>\n+      <when value="FeatureAgglomeration">\n+        <expand macro="estimator_params_text" label="Type in parameters:"\n+              help="Parameters in dictionary without braces (\'{}\'), e.g., \'n_clusters\': 2, \'affinity\': \'euclidean\'. No double quotes. Leave this box blank for class default."/>\n+      </when>\n+    </conditional>\n+  </xml>\n   <!-- Outputs -->\n \n   <xml name="output">\n@@ -1118,7 +1472,6 @@\n     </outputs>\n   </xml>\n \n-\n   <!--Citations-->\n   <xml name="eden_citation">\n     <citations>\n'
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diff -r f0e215cbade3 -r 8ccc9b001a88 test-data/feature_selection_result01
--- a/test-data/feature_selection_result01 Fri Jul 13 03:56:33 2018 -0400
+++ b/test-data/feature_selection_result01 Sat Aug 04 12:30:07 2018 -0400
b
@@ -1,262 +1,11 @@
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diff -r f0e215cbade3 -r 8ccc9b001a88 test-data/feature_selection_result08
--- a/test-data/feature_selection_result08 Fri Jul 13 03:56:33 2018 -0400
+++ b/test-data/feature_selection_result08 Sat Aug 04 12:30:07 2018 -0400
b
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b
diff -r f0e215cbade3 -r 8ccc9b001a88 test-data/feature_selection_result09
--- a/test-data/feature_selection_result09 Fri Jul 13 03:56:33 2018 -0400
+++ b/test-data/feature_selection_result09 Sat Aug 04 12:30:07 2018 -0400
b
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