Loris tutorial #2
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
| @@ -0,0 +1 @@ | |||
| {"a_galaxy_workflow": "true", "annotation": "Reproducing the model published by Chang et al, 2024 (https://www.nature.com/articles/s43018-024-00772-7)", "comments": [], "creator": [{"class": "Person", "identifier": "https://orcid.org/0000-0002-4403-6684", "name": "Paulo Cilas Morais Lyra Junior"}], "format-version": "0.1", "name": "LORIS model build", "report": {"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"}, "steps": {"0": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0", "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Pipeline Builder", "outputs": [{"name": "outfile", "type": "h5mlm"}], "position": {"left": 0.0, "top": 194.54691424684538}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0", "tool_shed_repository": {"changeset_revision": "4c4ec859c31a", "name": "sklearn_build_pipeline", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"final_estimator\": {\"estimator_selector\": {\"selected_module\": \"linear_model\", \"__current_case__\": 1, \"selected_estimator\": \"LogisticRegression\", \"text_params\": \"penalty='elasticnet', solver='saga', l1_ratio=1, class_weight='balanced', C=0.1, max_iter=100\"}}, \"pipeline_component\": [{\"__index__\": 0, \"component_selector\": {\"component_type\": \"pre_processor\", \"__current_case__\": 1, \"pre_processors\": {\"selected_pre_processor\": \"StandardScaler\", \"__current_case__\": 1, \"options\": {\"copy\": true, \"with_mean\": true, \"with_std\": true}}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "8f731f6c-da18-46db-ac8f-54d40d1eb997", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_train_Response.tsv"}], "label": "Chowell_train_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 155.40353732525276, "top": 304.1094244003058}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "9e597857-1618-490d-8bdd-c0a9af2301f9", "when": null, "workflow_outputs": []}, "2": {"annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_test_No_Response.tsv"}], "label": "Chowell_test_No_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 844.271830808547, "top": 34.1113101129842}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "77d160d7-d70f-48ec-8cb4-366c9c88fdc6", "when": null, "workflow_outputs": []}, "3": {"annotation": "", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [{"description": "", "name": "MSK1_No_Response.tsv"}], "label": "MSK1_No_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 862.1787974884945, "top": 701.6991791595183}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "d3f4e44b-1997-4320-a0c8-02114e82fe92", "when": null, "workflow_outputs": []}, "4": {"annotation": "", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_test_Response.tsv"}], "label": "Chowell_test_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 1614.8540700591673, "top": 29.432572336700446}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f4d423b6-4d64-4cb0-97a3-674ae8ac3397", "when": null, "workflow_outputs": []}, "5": {"annotation": "", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [{"description": "", "name": "MSK1_Response.tsv"}], "label": "MSK1_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 1610.0404015371512, "top": 773.2710560011026}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "2d619e0a-aaf9-426e-a804-1fd75965da9f", "when": null, "workflow_outputs": []}, "6": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0", "errors": null, "id": 6, "input_connections": {"infile_estimator": {"id": 0, "output_name": "outfile"}, "input_options|infile1": {"id": 1, "output_name": "output"}, "input_options|infile2": {"id": 1, "output_name": "output"}}, "inputs": [{"description": "runtime parameter for tool Hyperparameter Search", "name": "input_options"}, {"description": "runtime parameter for tool Hyperparameter Search", "name": "input_options"}], "label": null, "name": "Hyperparameter Search", "outputs": [{"name": "outfile_result", "type": "tabular"}, {"name": "outfile_object", "type": "h5mlm"}], "position": {"left": 645.6298202768934, "top": 172.85294629692783}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0", "tool_shed_repository": {"changeset_revision": "7626ea9c2e1b", "name": "sklearn_searchcv", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_estimator\": {\"__class__\": \"ConnectedValue\"}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"header1\": true, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_but_by_index_number\", \"__current_case__\": 1, \"col1\": [\"22\"]}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"header2\": true, \"column_selector_options_2\": {\"selected_column_selector_option2\": \"by_index_number\", \"__current_case__\": 0, \"col2\": \"22\"}}, \"is_deep_learning\": false, \"options\": {\"scoring\": {\"primary_scoring\": \"default\", \"__current_case__\": 0}, \"cv_selector\": {\"selected_cv\": \"default\", \"__current_case__\": 0, \"n_splits\": \"5\"}, \"verbose\": \"0\", \"error_score\": true, \"return_train_score\": false}, \"outer_split\": {\"split_mode\": \"no\", \"__current_case__\": 0}, \"save\": \"save_estimator\", \"search_algos\": {\"selected_search_algo\": \"GridSearchCV\", \"__current_case__\": 0}, \"search_params_builder\": {\"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_list\": \"\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "f5fbb971-75fd-478e-a0d5-0b5d4c18b236", "when": null, "workflow_outputs": []}, "7": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 7, "input_connections": {"input": {"id": 4, "output_name": "output"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1930.9230584574464, "top": 28.663859036723238}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "92a791c9-80df-44b1-ba1f-9fcd88d64c67", "when": null, "workflow_outputs": []}, "8": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 8, "input_connections": {"input": {"id": 5, "output_name": "output"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1913.018356314146, "top": 773.6518550649007}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "cefcc407-8919-4c88-8d69-f53a73b8e1f6", "when": null, "workflow_outputs": []}, "9": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "errors": null, "id": 9, "input_connections": {"selected_tasks|infile_data": {"id": 2, "output_name": "output"}, "selected_tasks|infile_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [{"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}, {"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}], "label": null, "name": "Ensemble methods", "outputs": [{"name": "outfile_predict", "type": "tabular"}], "position": {"left": 1259.9638931669028, "top": 0}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "tool_shed_repository": {"changeset_revision": "060ca94ac049", "name": "sklearn_ensemble", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"selected_tasks\": {\"selected_task\": \"load\", \"__current_case__\": 0, \"infile_model\": {\"__class__\": \"ConnectedValue\"}, \"infile_data\": {\"__class__\": \"ConnectedValue\"}, \"header\": true, \"prediction_options\": {\"prediction_option\": \"predict\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "7abd0e96-97c8-4fdc-af31-23a04a037d06", "when": null, "workflow_outputs": []}, "10": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "errors": null, "id": 10, "input_connections": {"selected_tasks|infile_data": {"id": 3, "output_name": "output"}, "selected_tasks|infile_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [{"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}, {"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}], "label": null, "name": "Ensemble methods", "outputs": [{"name": "outfile_predict", "type": "tabular"}], "position": {"left": 1259.0172533597843, "top": 671.2028500765132}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "tool_shed_repository": {"changeset_revision": "060ca94ac049", "name": "sklearn_ensemble", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"selected_tasks\": {\"selected_task\": \"load\", \"__current_case__\": 0, \"infile_model\": {\"__class__\": \"ConnectedValue\"}, \"infile_data\": {\"__class__\": \"ConnectedValue\"}, \"header\": true, \"prediction_options\": {\"prediction_option\": \"predict\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "97a1ae40-f5ff-4425-8b93-401835ad144d", "when": null, "workflow_outputs": []}, "11": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 11, "input_connections": {"input": {"id": 9, "output_name": "outfile_predict"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1610.2713342835384, "top": 164.01981206451842}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "35baa417-593f-41ec-8ff2-b1d67c269a02", "when": null, "workflow_outputs": []}, "12": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 12, "input_connections": {"input": {"id": 10, "output_name": "outfile_predict"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1615.4573157647017, "top": 613.868684929153}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "939cedd8-c82c-4fe2-b138-95da605139cf", "when": null, "workflow_outputs": []}, "13": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "errors": null, "id": 13, "input_connections": {"infile_input": {"id": 7, "output_name": "out_file1"}, "infile_output": {"id": 11, "output_name": "out_file1"}, "infile_trained_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [], "label": null, "name": "Plot confusion matrix, precision, recall and ROC and AUC curves", "outputs": [{"name": "output_confusion", "type": "png"}, {"name": "output_prf", "type": "html"}, {"name": "output_roc", "type": "html"}], "position": {"left": 2260.002304947657, "top": 125.5526410056442}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "tool_shed_repository": {"changeset_revision": "f234e2e59d76", "name": "plotly_ml_performance_plots", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_input\": {\"__class__\": \"ConnectedValue\"}, \"infile_output\": {\"__class__\": \"ConnectedValue\"}, \"infile_trained_model\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.4", "type": "tool", "uuid": "5cb8214f-1e1b-4605-88f8-fb502e29eb96", "when": null, "workflow_outputs": []}, "14": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "errors": null, "id": 14, "input_connections": {"infile_input": {"id": 8, "output_name": "out_file1"}, "infile_output": {"id": 12, "output_name": "out_file1"}, "infile_trained_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [], "label": null, "name": "Plot confusion matrix, precision, recall and ROC and AUC curves", "outputs": [{"name": "output_confusion", "type": "png"}, {"name": "output_prf", "type": "html"}, {"name": "output_roc", "type": "html"}], "position": {"left": 2260.172726744564, "top": 468.727041301727}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "tool_shed_repository": {"changeset_revision": "f234e2e59d76", "name": "plotly_ml_performance_plots", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_input\": {\"__class__\": \"ConnectedValue\"}, \"infile_output\": {\"__class__\": \"ConnectedValue\"}, \"infile_trained_model\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.4", "type": "tool", "uuid": "601084bd-e74f-449e-ac70-7f18f1232b7f", "when": null, "workflow_outputs": []}}, "tags": ["MachineLearning", "LORIS", "LogisticRegression", "MLModel"], "uuid": "7bdb88c2-ee05-4068-be31-2766369e6a5a", "version": 3} | |||
There was a problem hiding this comment.
🚫 [rdjsonl] <GTN:027> reported by reviewdog 🐶
This workflow is missing a test, which is now mandatory. Please see the FAQ on how to add tests to your workflows.
| @@ -0,0 +1 @@ | |||
| {"a_galaxy_workflow": "true", "annotation": "Reproducing the model published by Chang et al, 2024 (https://www.nature.com/articles/s43018-024-00772-7)", "comments": [], "creator": [{"class": "Person", "identifier": "https://orcid.org/0000-0002-4403-6684", "name": "Paulo Cilas Morais Lyra Junior"}], "format-version": "0.1", "name": "LORIS model build", "report": {"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"}, "steps": {"0": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0", "errors": null, "id": 0, "input_connections": {}, "inputs": [], "label": null, "name": "Pipeline Builder", "outputs": [{"name": "outfile", "type": "h5mlm"}], "position": {"left": 0.0, "top": 194.54691424684538}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0.11.0", "tool_shed_repository": {"changeset_revision": "4c4ec859c31a", "name": "sklearn_build_pipeline", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"final_estimator\": {\"estimator_selector\": {\"selected_module\": \"linear_model\", \"__current_case__\": 1, \"selected_estimator\": \"LogisticRegression\", \"text_params\": \"penalty='elasticnet', solver='saga', l1_ratio=1, class_weight='balanced', C=0.1, max_iter=100\"}}, \"pipeline_component\": [{\"__index__\": 0, \"component_selector\": {\"component_type\": \"pre_processor\", \"__current_case__\": 1, \"pre_processors\": {\"selected_pre_processor\": \"StandardScaler\", \"__current_case__\": 1, \"options\": {\"copy\": true, \"with_mean\": true, \"with_std\": true}}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "8f731f6c-da18-46db-ac8f-54d40d1eb997", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_train_Response.tsv"}], "label": "Chowell_train_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 155.40353732525276, "top": 304.1094244003058}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "9e597857-1618-490d-8bdd-c0a9af2301f9", "when": null, "workflow_outputs": []}, "2": {"annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_test_No_Response.tsv"}], "label": "Chowell_test_No_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 844.271830808547, "top": 34.1113101129842}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "77d160d7-d70f-48ec-8cb4-366c9c88fdc6", "when": null, "workflow_outputs": []}, "3": {"annotation": "", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [{"description": "", "name": "MSK1_No_Response.tsv"}], "label": "MSK1_No_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 862.1787974884945, "top": 701.6991791595183}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "d3f4e44b-1997-4320-a0c8-02114e82fe92", "when": null, "workflow_outputs": []}, "4": {"annotation": "", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [{"description": "", "name": "Chowell_test_Response.tsv"}], "label": "Chowell_test_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 1614.8540700591673, "top": 29.432572336700446}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f4d423b6-4d64-4cb0-97a3-674ae8ac3397", "when": null, "workflow_outputs": []}, "5": {"annotation": "", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [{"description": "", "name": "MSK1_Response.tsv"}], "label": "MSK1_Response.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 1610.0404015371512, "top": 773.2710560011026}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "2d619e0a-aaf9-426e-a804-1fd75965da9f", "when": null, "workflow_outputs": []}, "6": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0", "errors": null, "id": 6, "input_connections": {"infile_estimator": {"id": 0, "output_name": "outfile"}, "input_options|infile1": {"id": 1, "output_name": "output"}, "input_options|infile2": {"id": 1, "output_name": "output"}}, "inputs": [{"description": "runtime parameter for tool Hyperparameter Search", "name": "input_options"}, {"description": "runtime parameter for tool Hyperparameter Search", "name": "input_options"}], "label": null, "name": "Hyperparameter Search", "outputs": [{"name": "outfile_result", "type": "tabular"}, {"name": "outfile_object", "type": "h5mlm"}], "position": {"left": 645.6298202768934, "top": 172.85294629692783}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0.11.0", "tool_shed_repository": {"changeset_revision": "7626ea9c2e1b", "name": "sklearn_searchcv", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_estimator\": {\"__class__\": \"ConnectedValue\"}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"header1\": true, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_but_by_index_number\", \"__current_case__\": 1, \"col1\": [\"22\"]}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"header2\": true, \"column_selector_options_2\": {\"selected_column_selector_option2\": \"by_index_number\", \"__current_case__\": 0, \"col2\": \"22\"}}, \"is_deep_learning\": false, \"options\": {\"scoring\": {\"primary_scoring\": \"default\", \"__current_case__\": 0}, \"cv_selector\": {\"selected_cv\": \"default\", \"__current_case__\": 0, \"n_splits\": \"5\"}, \"verbose\": \"0\", \"error_score\": true, \"return_train_score\": false}, \"outer_split\": {\"split_mode\": \"no\", \"__current_case__\": 0}, \"save\": \"save_estimator\", \"search_algos\": {\"selected_search_algo\": \"GridSearchCV\", \"__current_case__\": 0}, \"search_params_builder\": {\"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_list\": \"\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "f5fbb971-75fd-478e-a0d5-0b5d4c18b236", "when": null, "workflow_outputs": []}, "7": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 7, "input_connections": {"input": {"id": 4, "output_name": "output"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1930.9230584574464, "top": 28.663859036723238}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "92a791c9-80df-44b1-ba1f-9fcd88d64c67", "when": null, "workflow_outputs": []}, "8": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 8, "input_connections": {"input": {"id": 5, "output_name": "output"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1913.018356314146, "top": 773.6518550649007}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "cefcc407-8919-4c88-8d69-f53a73b8e1f6", "when": null, "workflow_outputs": []}, "9": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "errors": null, "id": 9, "input_connections": {"selected_tasks|infile_data": {"id": 2, "output_name": "output"}, "selected_tasks|infile_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [{"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}, {"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}], "label": null, "name": "Ensemble methods", "outputs": [{"name": "outfile_predict", "type": "tabular"}], "position": {"left": 1259.9638931669028, "top": 0}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "tool_shed_repository": {"changeset_revision": "060ca94ac049", "name": "sklearn_ensemble", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"selected_tasks\": {\"selected_task\": \"load\", \"__current_case__\": 0, \"infile_model\": {\"__class__\": \"ConnectedValue\"}, \"infile_data\": {\"__class__\": \"ConnectedValue\"}, \"header\": true, \"prediction_options\": {\"prediction_option\": \"predict\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "7abd0e96-97c8-4fdc-af31-23a04a037d06", "when": null, "workflow_outputs": []}, "10": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "errors": null, "id": 10, "input_connections": {"selected_tasks|infile_data": {"id": 3, "output_name": "output"}, "selected_tasks|infile_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [{"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}, {"description": "runtime parameter for tool Ensemble methods", "name": "selected_tasks"}], "label": null, "name": "Ensemble methods", "outputs": [{"name": "outfile_predict", "type": "tabular"}], "position": {"left": 1259.0172533597843, "top": 671.2028500765132}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0.11.0", "tool_shed_repository": {"changeset_revision": "060ca94ac049", "name": "sklearn_ensemble", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"selected_tasks\": {\"selected_task\": \"load\", \"__current_case__\": 0, \"infile_model\": {\"__class__\": \"ConnectedValue\"}, \"infile_data\": {\"__class__\": \"ConnectedValue\"}, \"header\": true, \"prediction_options\": {\"prediction_option\": \"predict\", \"__current_case__\": 0}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.11.0", "type": "tool", "uuid": "97a1ae40-f5ff-4425-8b93-401835ad144d", "when": null, "workflow_outputs": []}, "11": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 11, "input_connections": {"input": {"id": 9, "output_name": "outfile_predict"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1610.2713342835384, "top": 164.01981206451842}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "35baa417-593f-41ec-8ff2-b1d67c269a02", "when": null, "workflow_outputs": []}, "12": {"annotation": "", "content_id": "Remove beginning1", "errors": null, "id": 12, "input_connections": {"input": {"id": 10, "output_name": "outfile_predict"}}, "inputs": [], "label": null, "name": "Remove beginning", "outputs": [{"name": "out_file1", "type": "input"}], "position": {"left": 1615.4573157647017, "top": 613.868684929153}, "post_job_actions": {}, "tool_id": "Remove beginning1", "tool_state": "{\"__input_ext\": \"tabular\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"num_lines\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "939cedd8-c82c-4fe2-b138-95da605139cf", "when": null, "workflow_outputs": []}, "13": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "errors": null, "id": 13, "input_connections": {"infile_input": {"id": 7, "output_name": "out_file1"}, "infile_output": {"id": 11, "output_name": "out_file1"}, "infile_trained_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [], "label": null, "name": "Plot confusion matrix, precision, recall and ROC and AUC curves", "outputs": [{"name": "output_confusion", "type": "png"}, {"name": "output_prf", "type": "html"}, {"name": "output_roc", "type": "html"}], "position": {"left": 2260.002304947657, "top": 125.5526410056442}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "tool_shed_repository": {"changeset_revision": "f234e2e59d76", "name": "plotly_ml_performance_plots", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_input\": {\"__class__\": \"ConnectedValue\"}, \"infile_output\": {\"__class__\": \"ConnectedValue\"}, \"infile_trained_model\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.4", "type": "tool", "uuid": "5cb8214f-1e1b-4605-88f8-fb502e29eb96", "when": null, "workflow_outputs": []}, "14": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "errors": null, "id": 14, "input_connections": {"infile_input": {"id": 8, "output_name": "out_file1"}, "infile_output": {"id": 12, "output_name": "out_file1"}, "infile_trained_model": {"id": 6, "output_name": "outfile_object"}}, "inputs": [], "label": null, "name": "Plot confusion matrix, precision, recall and ROC and AUC curves", "outputs": [{"name": "output_confusion", "type": "png"}, {"name": "output_prf", "type": "html"}, {"name": "output_roc", "type": "html"}], "position": {"left": 2260.172726744564, "top": 468.727041301727}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.4", "tool_shed_repository": {"changeset_revision": "f234e2e59d76", "name": "plotly_ml_performance_plots", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"infile_input\": {\"__class__\": \"ConnectedValue\"}, \"infile_output\": {\"__class__\": \"ConnectedValue\"}, \"infile_trained_model\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.4", "type": "tool", "uuid": "601084bd-e74f-449e-ac70-7f18f1232b7f", "when": null, "workflow_outputs": []}}, "tags": ["MachineLearning", "LORIS", "LogisticRegression", "MLModel"], "uuid": "7bdb88c2-ee05-4068-be31-2766369e6a5a", "version": 3} | |||
|
|
||
| > <hands-on-title> Task description </hands-on-title> | ||
| > | ||
| > 1. {% tool [PyCaret Model Comparison](https://toolshed.g2.bx.psu.edu/repos/paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison/2024.3.3.2+0) %} with the following parameters: |
There was a problem hiding this comment.
🚫 [rdjsonl] <GTN:009> reported by reviewdog 🐶
You have used the full tool URL to a specific server, here we only need the tool ID portion.
Suggested change
| > 1. {% tool [PyCaret Model Comparison](https://toolshed.g2.bx.psu.edu/repos/paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison/2024.3.3.2+0) %} with the following parameters: | |
| > 1. {% tool [PyCaret Model Comparison](.bx.psu.edu/repos/paulo_lyra_jr/pycaret_model_comparison/PyCaret_Model_Comparison/2024.3.3.2+0) %} with the following parameters: |
| > 2. Import the files from Zenodo or from the shared data library | ||
| > | ||
| > ``` | ||
| > https://zenodo.org/api/records/13885908/files/Chowell_train_Response.tsv |
| > | ||
| > ``` | ||
| > https://zenodo.org/api/records/13885908/files/Chowell_train_Response.tsv | ||
| > https://zenodo.org/api/records/13885908/files/Chowell_test_Response.tsv |
paulocilasjr
pushed a commit
that referenced
this pull request
Nov 21, 2024
…st (#2) Co-authored-by: dianichj <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Loris