test sklearn_searchcv/1.0.8.4

[jennaj]

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.4

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.8.4

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.8.4

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	13
Passed	12
Error	0
Failure	1
Skipped	0

Failed s

• ❌ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)

  Problems:

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.8.4, exit_code: 1, stderr: /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    Traceback (most recent call last):
      File "/corral4/main/jobs/050/032/50032528/configs/tmpj0jsqndb", line 68, in <module>
        new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
      File "/usr/local/lib/python3.6/site-packages/galaxy_ml/utils.py", line 256, in feature_selector
        options['cv'] = list(splitter.split(X, y, groups=groups))
      File "/usr/local/lib/python3.6/site-packages/sklearn/model_selection/_split.py", line 1322, in split
        X, y, groups = indexable(X, y, groups)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 230, in indexable
        check_consistent_length(*result)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 205, in check_consistent_length
        " samples: %r" % [int(l) for l in lengths])
    ValueError: Found input variables with inconsistent numbers of samples: [261, 261, 10]
    .
    

  • Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.8.4, exit_code: 1, stderr: /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    Traceback (most recent call last):
      File "/corral4/main/jobs/050/032/50032528/configs/tmpj0jsqndb", line 68, in <module>
        new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
      File "/usr/local/lib/python3.6/site-packages/galaxy_ml/utils.py", line 256, in feature_selector
        options['cv'] = list(splitter.split(X, y, groups=groups))
      File "/usr/local/lib/python3.6/site-packages/sklearn/model_selection/_split.py", line 1322, in split
        X, y, groups = indexable(X, y, groups)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 230, in indexable
        check_consistent_length(*result)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 205, in check_consistent_length
        " samples: %r" % [int(l) for l in lengths])
    ValueError: Found input variables with inconsistent numbers of samples: [261, 261, 10]
    .
    

  Command Line:

  Exit Code:

  • 1

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    Traceback (most recent call last):
      File "/corral4/main/jobs/050/032/50032528/configs/tmpj0jsqndb", line 68, in <module>
        new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
      File "/usr/local/lib/python3.6/site-packages/galaxy_ml/utils.py", line 256, in feature_selector
        options['cv'] = list(splitter.split(X, y, groups=groups))
      File "/usr/local/lib/python3.6/site-packages/sklearn/model_selection/_split.py", line 1322, in split
        X, y, groups = indexable(X, y, groups)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 230, in indexable
        check_consistent_length(*result)
      File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 205, in check_consistent_length
        " samples: %r" % [int(l) for l in lengths])
    ValueError: Found input variables with inconsistent numbers of samples: [261, 261, 10]
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 9, "estimator_selector": {"__current_case__": 2, "selected_estimator": "RandomForestRegressor", "selected_module": "ensemble", "text_params": "n_estimators=10, random_state=10"}, "options": {"cv_selector": {"__current_case__": 14, "groups_selector": {"column_selector_options_g": {"__current_case__": 0, "col_g": "1", "selected_column_selector_option_g": "by_index_number"}, "header_g": true, "infile_g": {"values": [{"id": 111470611, "src": "hda"}]}}, "n_splits": "5", "random_state": "0", "selected_cv": "GroupShuffleSplit", "test_size": "0.2"}, "min_features_to_select": "1", "scoring": {"__current_case__": 0, "primary_scoring": "default"}, "step": "1.0", "verbose": "0"}, "selected_algorithm": "RFECV"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470593, "src": "hda"}]}, "infile2": {"values": [{"id": 111470594, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 7, "model_inputter": {"__current_case__": 0, "estimator_selector": {"__current_case__": 2, "selected_estimator": "RandomForestRegressor", "selected_module": "ensemble", "text_params": "n_estimators=10, random_state=10"}, "input_mode": "new"}, "options": {"max_features": "", "norm_order": "1", "threshold": ""}, "selected_algorithm": "SelectFromModel"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "6", "selected_column_selector_option2": "by_index_number"}, "header1": false, "header2": false, "infile1": {"values": [{"id": 111470547, "src": "hda"}]}, "infile2": {"values": [{"id": 111470547, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 0, "options": {"mode": "percentile", "param": "20.0"}, "score_func": "chi2", "selected_algorithm": "GenericUnivariateSelect"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test racon 1.3.1.1 #11)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 2, "options": {"k": "3"}, "score_func": "chi2", "selected_algorithm": "SelectKBest"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 3, "col1": "target", "selected_column_selector_option": "all_but_by_header_name"}, "column_selector_options_2": {"__current_case__": 2, "col2": "target", "selected_column_selector_option2": "by_header_name"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470588, "src": "hda"}]}, "infile2": {"values": [{"id": 111470588, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test mafft 7.221.3 #12)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 7, "model_inputter": {"__current_case__": 1, "fitted_estimator": {"values": [{"id": 111470591, "src": "hda"}]}, "input_mode": "prefitted"}, "options": {"max_features": "", "norm_order": "1", "threshold": ""}, "selected_algorithm": "SelectFromModel"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": false, "header2": false, "infile1": {"values": [{"id": 111470592, "src": "hda"}]}, "infile2": {"values": [{"id": 111470592, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 1, "options": {"percentile": "10"}, "score_func": "chi2", "selected_algorithm": "SelectPercentile"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 2, "options": {"k": "10"}, "score_func": "chi2", "selected_algorithm": "SelectKBest"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 3, "options": {"alpha": "0.05"}, "score_func": "chi2", "selected_algorithm": "SelectFpr"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test trinotate 3.2.2+galaxy0 #6)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 4, "options": {"alpha": "0.05"}, "score_func": "chi2", "selected_algorithm": "SelectFdr"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test pangolin 3.1.17+galaxy1 #7)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 5, "options": {"alpha": "0.05"}, "score_func": "chi2", "selected_algorithm": "SelectFwe"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470548, "src": "hda"}]}, "infile2": {"values": [{"id": 111470554, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 8, "estimator_selector": {"__current_case__": 2, "selected_estimator": "RandomForestRegressor", "selected_module": "ensemble", "text_params": "n_estimators=10, random_state=10"}, "options": {"n_features_to_select": "", "step": "1.0", "verbose": "0"}, "selected_algorithm": "RFE"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "6", "selected_column_selector_option2": "by_index_number"}, "header1": false, "header2": false, "infile1": {"values": [{"id": 111470592, "src": "hda"}]}, "infile2": {"values": [{"id": 111470592, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test gffread 2.2.1.3+galaxy0 #9)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 9, "estimator_selector": {"__current_case__": 2, "selected_estimator": "RandomForestRegressor", "selected_module": "ensemble", "text_params": "n_estimators=10, random_state=10"}, "options": {"cv_selector": {"__current_case__": 0, "n_splits": "3", "selected_cv": "default"}, "min_features_to_select": "1", "scoring": {"__current_case__": 0, "primary_scoring": "default"}, "step": "1.0", "verbose": "0"}, "selected_algorithm": "RFECV"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "6", "selected_column_selector_option2": "by_index_number"}, "header1": false, "header2": false, "infile1": {"values": [{"id": 111470547, "src": "hda"}]}, "infile2": {"values": [{"id": 111470547, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection (Test Test trim_galore 0.6.7+galaxy0 #10)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    Using TensorFlow backend.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    fs_algorithm_selector	{"__current_case__": 6, "options": {"threshold": "0.1"}, "selected_algorithm": "VarianceThreshold"}
    save	false
    input_options	{"__current_case__": 0, "column_selector_options_1": {"__current_case__": 0, "col1": ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17"], "selected_column_selector_option": "by_index_number"}, "column_selector_options_2": {"__current_case__": 0, "col2": "1", "selected_column_selector_option2": "by_index_number"}, "header1": true, "header2": true, "infile1": {"values": [{"id": 111470593, "src": "hda"}]}, "infile2": {"values": [{"id": 111470594, "src": "hda"}]}, "selected_input": "tabular"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

[jennaj]

test failed, but for an input issue with the test data. the tests probably do not check for the option used by the user who wrote into bugs.

Job in error state.. tool_id:

toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.8.4, exit_code: 1, stderr: /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
warnings.warn(msg, category=DeprecationWarning)
Using TensorFlow backend.
Traceback (most recent call last):
File "/corral4/main/jobs/050/032/50032528/configs/tmpj0jsqndb", line 68, in
new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
File "/usr/local/lib/python3.6/site-packages/galaxy_ml/utils.py", line 256, in feature_selector
options['cv'] = list(splitter.split(X, y, groups=groups))
File "/usr/local/lib/python3.6/site-packages/sklearn/model_selection/_split.py", line 1322, in split
X, y, groups = indexable(X, y, groups)
File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 230, in indexable
check_consistent_length(*result)
File "/usr/local/lib/python3.6/site-packages/sklearn/utils/validation.py", line 205, in check_consistent_length
" samples: %r" % [int(l) for l in lengths])
ValueError: Found input variables with inconsistent numbers of samples: [261, 261, 10]

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca/1.0.8.4+galaxy0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	6
Passed	6
Error	0
Failure	0
Skipped	0

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 5, 'svd_solver': 'arpack', 'whiten': False, 'tol': 0.4}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	false
    column_selector_options	{"__current_case__": 0, "col1": ["1", "2", "4", "6", "8", "5"], "selected_column_selector_option": "by_index_number"}
    select_pca_type	{"__current_case__": 0, "number": "5", "select_pca_opts": "classical", "select_solver_type": {"__current_case__": 0, "svd_solver_opts": "arpack", "tolerance": "0.4"}, "whiten": false}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 5, 'svd_solver': 'arpack', 'whiten': False, 'tol': 0.4}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	true
    column_selector_options	{"__current_case__": 2, "col1": "col_1,col_2,col_4,col_6,col_8,col_5", "selected_column_selector_option": "by_header_name"}
    select_pca_type	{"__current_case__": 0, "number": "5", "select_pca_opts": "classical", "select_solver_type": {"__current_case__": 0, "svd_solver_opts": "arpack", "tolerance": "0.4"}, "whiten": false}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 7, 'batch_size': 64, 'whiten': False}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	false
    column_selector_options	{"__current_case__": 1, "col1": ["8", "5"], "selected_column_selector_option": "all_but_by_index_number"}
    select_pca_type	{"__current_case__": 1, "batch_size": "64", "number": "7", "select_pca_opts": "incremental", "whiten": false}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 7, 'batch_size': 64, 'whiten': False}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	true
    column_selector_options	{"__current_case__": 3, "col1": "col_8,col_5", "selected_column_selector_option": "all_but_by_header_name"}
    select_pca_type	{"__current_case__": 1, "batch_size": "64", "number": "7", "select_pca_opts": "incremental", "whiten": false}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 8, 'kernel': 'linear', 'eigen_solver': 'arpack', 'gamma': None, 'tol': 4.3, 'max_iter': 8}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	false
    column_selector_options	{"__current_case__": 4, "selected_column_selector_option": "all_columns"}
    select_pca_type	{"__current_case__": 2, "number": "8", "select_kernel_opts": {"__current_case__": 3, "kernel_opts": "linear"}, "select_pca_opts": "kernel", "select_solver_type": {"__current_case__": 0, "eigen_solver_opts": "arpack", "max_iter": "8", "tolerance": "4.3"}}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"

• ✅ toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pca/sklearn_pca (Test Test trinotate 3.2.2+galaxy0 #6)

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • Using TensorFlow backend.
    /usr/local/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
      warnings.warn(msg, category=DeprecationWarning)
    

  Standard Output:

  • {'n_components': 8, 'kernel': 'poly', 'eigen_solver': 'auto', 'gamma': 0.3, 'degree': 4, 'coef0': 1.6}
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    header	false
    column_selector_options	{"__current_case__": 4, "selected_column_selector_option": "all_columns"}
    select_pca_type	{"__current_case__": 2, "number": "8", "select_kernel_opts": {"__current_case__": 0, "coef0": "1.6", "degree": "4", "gamma": "0.3", "kernel_opts": "poly"}, "select_pca_opts": "kernel", "select_solver_type": {"__current_case__": 1, "eigen_solver_opts": "auto"}}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"input"