From f6fe5628d85d4263477b72d8c1ded5ab473fb97a Mon Sep 17 00:00:00 2001 From: Kaivan Kamali Date: Wed, 24 Jan 2024 12:00:36 -0500 Subject: [PATCH] Fixed the extra WF step. Fixed instructions in model prediction --- topics/statistics/tutorials/RNN/tutorial.md | 1 - .../RNN/workflows/Intro_To_RNN_v1_0_10_0.ga | 168 +++++++++--------- 2 files changed, 86 insertions(+), 83 deletions(-) diff --git a/topics/statistics/tutorials/RNN/tutorial.md b/topics/statistics/tutorials/RNN/tutorial.md index 720e51fdc2087c..805bd7f64f3903 100644 --- a/topics/statistics/tutorials/RNN/tutorial.md +++ b/topics/statistics/tutorials/RNN/tutorial.md @@ -327,7 +327,6 @@ The training step generates 2 datasets. 1) accuracy of the trained model, 2) the > > - {% tool [Model Prediction](toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0) %} > - *"Choose the dataset containing pipeline/estimator object"* : Select the trained model from the previous step. -> - *"Choose the dataset containing weights for the estimator above"* : Select the trained model weights from the previous step. > - *"Select invocation method"*: `predict` > - *"Select input data type for prediction"*: `tabular data` > - *"Training samples dataset"*: Select `X_test` dataset diff --git a/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga b/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga index 3d7ecca77e7af4..c8e51adb4092f3 100644 --- a/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga +++ b/topics/statistics/tutorials/RNN/workflows/Intro_To_RNN_v1_0_10_0.ga @@ -1,7 +1,14 @@ { "a_galaxy_workflow": "true", "annotation": "", - "creator": [{"class": "Person", "identifier":"0000-0001-6585-3619", "name": "Kaivan Kamali"}], + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "0000-0001-6585-3619", + "name": "Kaivan Kamali" + } + ], "format-version": "0.1", "license": "CC-BY-4.0", "name": "Intro_To_RNN_v1_0_10_0", @@ -22,8 +29,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 10 + "left": 0, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -49,8 +56,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 130 + "left": 0, + "top": 120 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -76,8 +83,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 250 + "left": 0, + "top": 240 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -103,8 +110,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 10, - "top": 370 + "left": 0, + "top": 360 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", @@ -130,8 +137,8 @@ } ], "position": { - "left": 10, - "top": 490 + "left": 0, + "top": 480 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/1.0.10.0", @@ -142,63 +149,29 @@ "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"model_selection\": {\"model_type\": \"sequential\", \"__current_case__\": 0, \"input_shape\": \"(500, )\", \"layers\": [{\"__index__\": 0, \"layer_selection\": {\"layer_type\": \"Embedding\", \"__current_case__\": 53, \"input_dim\": \"10000\", \"output_dim\": \"32\", \"kwargs\": \"\"}}, {\"__index__\": 1, \"layer_selection\": {\"layer_type\": \"LSTM\", \"__current_case__\": 45, \"units\": \"100\", \"kwargs\": \"\"}}, {\"__index__\": 2, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"1\", \"activation\": \"sigmoid\", \"kwargs\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_version": "1.0.10.0", "type": "tool", "uuid": "f61aba17-35c3-4990-acb9-0e96b0979e7c", "when": null, "workflow_outputs": [] }, "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3", - "errors": null, - "id": 5, - "input_connections": { - "plotting_selection|infile_true": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Machine Learning Visualization Extension", - "outputs": [ - { - "name": "output", - "type": "html" - } - ], - "position": { - "left": 230, - "top": 10 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3", - "tool_shed_repository": { - "changeset_revision": "947c2eacccb8", - "name": "ml_visualization_ex", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__input_ext\": \"input\", \"__workflow_invocation_uuid__\": \"75b2007ed24c11edba82005056ba2773\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"plotting_selection\": {\"plot_type\": \"classification_confusion_matrix\", \"__current_case__\": 6, \"infile_true\": null, \"header_true\": false, \"column_selector_options_true\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile_predicted\": null, \"header_predicted\": true, \"title\": \"Confusion matrix between true and predicted labels\", \"plot_format\": \"png\", \"plot_color\": \"Greens\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, - "type": "tool", - "uuid": "62893cf8-21d5-4f12-b164-bf16d145843d", - "when": null, - "workflow_outputs": [] - }, - "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0", "errors": null, - "id": 6, + "id": 5, "input_connections": { "mode_selection|infile_json": { "id": 4, "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Create deep learning model", + "name": "mode_selection" + } + ], "label": null, "name": "Create deep learning model", "outputs": [ @@ -208,8 +181,8 @@ } ], "position": { - "left": 230, - "top": 130 + "left": 420.2373046875, + "top": 466.32183837890625 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/1.0.10.0", @@ -219,21 +192,21 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"mode_selection\": {\"mode_type\": \"train_model\", \"__current_case__\": 0, \"infile_json\": null, \"learning_type\": \"KerasGClassifier\", \"compile_params\": {\"loss\": \"binary_crossentropy\", \"optimizer_selection\": {\"optimizer_type\": \"Adam\", \"__current_case__\": 4, \"optimizer_options\": {\"learning_rate\": \"0.001\", \"beta_1\": \"0.9\", \"beta_2\": \"0.999\", \"epsilon\": \"1e-07\", \"amsgrad\": false}}, \"metrics\": [\"acc\"]}, \"fit_params\": {\"epochs\": \"2\", \"batch_size\": \"128\", \"steps_per_epoch\": null, \"validation_split\": \"0.1\", \"validation_steps\": null, \"callbacks\": [{\"__index__\": 0, \"callback_selection\": {\"callback_type\": \"None\", \"__current_case__\": 0}}], \"verbose\": \"1\"}, \"random_seed\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"mode_selection\": {\"mode_type\": \"train_model\", \"__current_case__\": 0, \"infile_json\": {\"__class__\": \"ConnectedValue\"}, \"learning_type\": \"KerasGClassifier\", \"compile_params\": {\"loss\": \"binary_crossentropy\", \"optimizer_selection\": {\"optimizer_type\": \"Adam\", \"__current_case__\": 4, \"optimizer_options\": {\"learning_rate\": \"0.001\", \"beta_1\": \"0.9\", \"beta_2\": \"0.999\", \"epsilon\": \"1e-07\", \"amsgrad\": false}}, \"metrics\": [\"acc\"]}, \"fit_params\": {\"epochs\": \"2\", \"batch_size\": \"128\", \"steps_per_epoch\": null, \"validation_split\": \"0.1\", \"validation_steps\": null, \"callbacks\": [{\"__index__\": 0, \"callback_selection\": {\"callback_type\": \"None\", \"__current_case__\": 0}}], \"verbose\": \"1\"}, \"random_seed\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.10.0", "type": "tool", "uuid": "5d389aed-7cba-45bb-b635-526b6b6c12cb", "when": null, "workflow_outputs": [] }, - "7": { + "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0", "errors": null, - "id": 7, + "id": 6, "input_connections": { "experiment_schemes|infile_estimator": { - "id": 6, + "id": 5, "output_name": "outfile" }, "input_options|infile1": { @@ -245,7 +218,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Deep learning training and evaluation", + "name": "experiment_schemes" + }, + { + "description": "runtime parameter for tool Deep learning training and evaluation", + "name": "input_options" + }, + { + "description": "runtime parameter for tool Deep learning training and evaluation", + "name": "input_options" + } + ], "label": null, "name": "Deep learning training and evaluation", "outputs": [ @@ -259,8 +245,8 @@ } ], "position": { - "left": 450, - "top": 10 + "left": 440, + "top": 0 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.10.0", @@ -270,21 +256,21 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"experiment_schemes\": {\"selected_exp_scheme\": \"train_val\", \"__current_case__\": 0, \"infile_estimator\": null, \"hyperparams_swapping\": {\"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_value\": \"\"}]}, \"test_split\": {\"split_algos\": {\"shuffle\": \"simple\", \"__current_case__\": 1, \"test_size\": \"0.2\", \"random_state\": null}}, \"metrics\": {\"scoring\": {\"primary_scoring\": \"f1\", \"__current_case__\": 4, \"secondary_scoring\": null}}}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": null, \"header1\": false, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile2\": null, \"header2\": false, \"column_selector_options_2\": {\"selected_column_selector_option2\": \"all_columns\", \"__current_case__\": 4}}, \"save\": [\"save_estimator\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"experiment_schemes\": {\"selected_exp_scheme\": \"train_val\", \"__current_case__\": 0, \"infile_estimator\": {\"__class__\": \"ConnectedValue\"}, \"hyperparams_swapping\": {\"param_set\": [{\"__index__\": 0, \"sp_name\": null, \"sp_value\": \"\"}]}, \"test_split\": {\"split_algos\": {\"shuffle\": \"simple\", \"__current_case__\": 1, \"test_size\": \"0.2\", \"random_state\": null}}, \"metrics\": {\"scoring\": {\"primary_scoring\": \"f1\", \"__current_case__\": 4, \"secondary_scoring\": null}}}, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"header1\": false, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"header2\": false, \"column_selector_options_2\": {\"selected_column_selector_option2\": \"all_columns\", \"__current_case__\": 4}}, \"save\": [\"save_estimator\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.10.0", "type": "tool", "uuid": "ef36b0d2-4e0e-4247-8763-5b59eb2b859d", "when": null, "workflow_outputs": [] }, - "8": { + "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0", "errors": null, - "id": 8, + "id": 7, "input_connections": { "infile_estimator": { - "id": 7, + "id": 6, "output_name": "outfile_object" }, "input_options|infile1": { @@ -292,7 +278,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Model Prediction", + "name": "infile_estimator" + }, + { + "description": "runtime parameter for tool Model Prediction", + "name": "input_options" + } + ], "label": null, "name": "Model Prediction", "outputs": [ @@ -302,8 +297,8 @@ } ], "position": { - "left": 670, - "top": 10 + "left": 939.120849609375, + "top": 35.953182568359324 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.10.0", @@ -313,21 +308,21 @@ "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\": null, \"input_options\": {\"selected_input\": \"tabular\", \"__current_case__\": 0, \"infile1\": null, \"header1\": false, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}}, \"method\": \"predict\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "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\": false, \"column_selector_options_1\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}}, \"method\": \"predict\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.10.0", "type": "tool", "uuid": "84e00c86-0370-4232-b20d-1d54f8c00d6e", "when": null, "workflow_outputs": [] }, - "9": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0", "errors": null, - "id": 9, + "id": 8, "input_connections": { "plotting_selection|infile_predicted": { - "id": 8, + "id": 7, "output_name": "outfile_predict" }, "plotting_selection|infile_true": { @@ -335,7 +330,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Machine Learning Visualization Extension", + "name": "plotting_selection" + }, + { + "description": "runtime parameter for tool Machine Learning Visualization Extension", + "name": "plotting_selection" + } + ], "label": null, "name": "Machine Learning Visualization Extension", "outputs": [ @@ -345,8 +349,8 @@ } ], "position": { - "left": 890, - "top": 10 + "left": 1311.8768310546875, + "top": 34.11192321777344 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.10.0", @@ -356,8 +360,8 @@ "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"plotting_selection\": {\"plot_type\": \"classification_confusion_matrix\", \"__current_case__\": 6, \"infile_true\": null, \"header_true\": false, \"column_selector_options_true\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile_predicted\": null, \"header_predicted\": true, \"title\": \"Confusion matrix between true and predicted labels\", \"plot_format\": \"png\", \"plot_color\": \"Greens\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": null, + "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"plotting_selection\": {\"plot_type\": \"classification_confusion_matrix\", \"__current_case__\": 6, \"infile_true\": {\"__class__\": \"ConnectedValue\"}, \"header_true\": false, \"column_selector_options_true\": {\"selected_column_selector_option\": \"all_columns\", \"__current_case__\": 4}, \"infile_predicted\": {\"__class__\": \"ConnectedValue\"}, \"header_predicted\": true, \"title\": \"Confusion matrix between true and predicted labels\", \"plot_format\": \"png\", \"plot_color\": \"Greens\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.10.0", "type": "tool", "uuid": "46cc48a1-b1c9-49fe-9c3c-5996ed4cc592", "when": null, @@ -365,6 +369,6 @@ } }, "tags": [], - "uuid": "c995f5c8-de9c-4bc5-9a15-1060eb569d40", + "uuid": "a69429bf-5f8d-45e9-991f-f30786f62ab3", "version": 1 }