Update GTN workflows (#7)

Co-authored-by: bedroesb <[email protected]>

Author: github-actions[bot]

GTN/CNN_Intro_To_CNN.ga

@@ -0,0 +1,368 @@
+{
+  "a_galaxy_workflow": "true",
+  "annotation": "Introduction to CNN",
+  "format-version": "0.1",
+  "name": "Intro To CNN",
+  "steps": {
+    "0": {
+      "annotation": "",
+      "content_id": null,
+      "errors": null,
+      "id": 0,
+      "input_connections": {},
+      "inputs": [
+        {
+          "description": "",
+          "name": "X_train"
+        }
+      ],
+      "label": "X_train",
+      "name": "Input dataset",
+      "outputs": [],
+      "position": {
+        "left": 10,
+        "top": 10
+      },
+      "tool_id": null,
+      "tool_state": "{\"optional\": false}",
+      "tool_version": null,
+      "type": "data_input",
+      "uuid": "986e5a5a-39f1-4ffe-91e2-b7b789450cde",
+      "workflow_outputs": []
+    },
+    "1": {
+      "annotation": "",
+      "content_id": null,
+      "errors": null,
+      "id": 1,
+      "input_connections": {},
+      "inputs": [
+        {
+          "description": "",
+          "name": "y_train"
+        }
+      ],
+      "label": "y_train",
+      "name": "Input dataset",
+      "outputs": [],
+      "position": {
+        "left": 10,
+        "top": 130
+      },
+      "tool_id": null,
+      "tool_state": "{\"optional\": false}",
+      "tool_version": null,
+      "type": "data_input",
+      "uuid": "3eb2384b-9c80-4671-9c12-8085a10c9b89",
+      "workflow_outputs": []
+    },
+    "2": {
+      "annotation": "",
+      "content_id": null,
+      "errors": null,
+      "id": 2,
+      "input_connections": {},
+      "inputs": [
+        {
+          "description": "",
+          "name": "X_test"
+        }
+      ],
+      "label": "X_test",
+      "name": "Input dataset",
+      "outputs": [],
+      "position": {
+        "left": 10,
+        "top": 250
+      },
+      "tool_id": null,
+      "tool_state": "{\"optional\": false}",
+      "tool_version": null,
+      "type": "data_input",
+      "uuid": "1af66795-2568-40e9-be01-4b5e8d70bbe3",
+      "workflow_outputs": []
+    },
+    "3": {
+      "annotation": "",
+      "content_id": null,
+      "errors": null,
+      "id": 3,
+      "input_connections": {},
+      "inputs": [
+        {
+          "description": "",
+          "name": "y_test"
+        }
+      ],
+      "label": "y_test",
+      "name": "Input dataset",
+      "outputs": [],
+      "position": {
+        "left": 10,
+        "top": 370
+      },
+      "tool_id": null,
+      "tool_state": "{\"optional\": false}",
+      "tool_version": null,
+      "type": "data_input",
+      "uuid": "a31af6be-59e7-468f-9309-001ea659fad5",
+      "workflow_outputs": []
+    },
+    "4": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+      "errors": null,
+      "id": 4,
+      "input_connections": {},
+      "inputs": [],
+      "label": null,
+      "name": "Create a deep learning model architecture",
+      "outputs": [
+        {
+          "name": "outfile",
+          "type": "json"
+        }
+      ],
+      "position": {
+        "left": 10,
+        "top": 490
+      },
+      "post_job_actions": {},
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_config/keras_model_config/0.5.0",
+      "tool_shed_repository": {
+        "changeset_revision": "64bbfa592868",
+        "name": "keras_model_config",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"model_selection\": {\"model_type\": \"sequential\", \"__current_case__\": 0, \"input_shape\": \"(784, )\", \"layers\": [{\"__index__\": 0, \"layer_selection\": {\"layer_type\": \"Reshape\", \"__current_case__\": 4, \"target_shape\": \"(28,28,1)\"}}, {\"__index__\": 1, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"64\", \"kernel_size\": \"3\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 2, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 3, \"layer_selection\": {\"layer_type\": \"Conv2D\", \"__current_case__\": 13, \"filters\": \"32\", \"kernel_size\": \"3\", \"activation\": \"relu\", \"kwargs\": \"\"}}, {\"__index__\": 4, \"layer_selection\": {\"layer_type\": \"MaxPooling2D\", \"__current_case__\": 30, \"pool_size\": \"(2, 2)\", \"strides\": \"\", \"kwargs\": \"\"}}, {\"__index__\": 5, \"layer_selection\": {\"layer_type\": \"Flatten\", \"__current_case__\": 3, \"data_format\": \"channels_last\"}}, {\"__index__\": 6, \"layer_selection\": {\"layer_type\": \"Dense\", \"__current_case__\": 0, \"units\": \"10\", \"activation\": \"softmax\", \"kwargs\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+      "tool_version": "0.5.0",
+      "type": "tool",
+      "uuid": "eca0c4b0-39ec-4c40-85bb-1ff33a1d274d",
+      "workflow_outputs": []
+    },
+    "5": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+      "errors": null,
+      "id": 5,
+      "input_connections": {
+        "infile": {
+          "id": 1,
+          "output_name": "output"
+        }
+      },
+      "inputs": [],
+      "label": null,
+      "name": "To categorical",
+      "outputs": [
+        {
+          "name": "outfile",
+          "type": "tabular"
+        }
+      ],
+      "position": {
+        "left": 230,
+        "top": 10
+      },
+      "post_job_actions": {},
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_to_categorical/sklearn_to_categorical/1.0.8.3",
+      "tool_shed_repository": {
+        "changeset_revision": "59e8b4328c82",
+        "name": "sklearn_to_categorical",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"header0\": \"false\", \"infile\": null, \"num_classes\": \"10\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+      "tool_version": "1.0.8.3",
+      "type": "tool",
+      "uuid": "3aac83d4-57b8-4c08-bf23-70b667d54a10",
+      "workflow_outputs": []
+    },
+    "6": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+      "errors": null,
+      "id": 6,
+      "input_connections": {
+        "mode_selection|infile_json": {
+          "id": 4,
+          "output_name": "outfile"
+        }
+      },
+      "inputs": [],
+      "label": null,
+      "name": "Create deep learning model",
+      "outputs": [
+        {
+          "name": "outfile",
+          "type": "zip"
+        }
+      ],
+      "position": {
+        "left": 230,
+        "top": 130
+      },
+      "post_job_actions": {},
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/0.5.0",
+      "tool_shed_repository": {
+        "changeset_revision": "e3b420d0b71a",
+        "name": "keras_model_builder",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"mode_selection\": {\"mode_type\": \"train_model\", \"__current_case__\": 0, \"infile_json\": null, \"learning_type\": \"KerasGClassifier\", \"compile_params\": {\"loss\": \"categorical_crossentropy\", \"optimizer_selection\": {\"optimizer_type\": \"Adam\", \"__current_case__\": 4, \"optimizer_options\": {\"lr\": \"0.001\", \"decay\": \"0.0\", \"beta_1\": \"0.9\", \"beta_2\": \"0.999\", \"amsgrad\": \"false\"}}, \"metrics\": [\"acc\"]}, \"fit_params\": {\"epochs\": \"10\", \"batch_size\": \"500\", \"steps_per_epoch\": null, \"validation_steps\": null, \"callbacks\": [{\"__index__\": 0, \"callback_selection\": {\"callback_type\": \"None\", \"__current_case__\": 0}}]}, \"random_seed\": null, \"get_params\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+      "tool_version": "0.5.0",
+      "type": "tool",
+      "uuid": "471d5906-3c94-4a41-b0a7-938bac5f2580",
+      "workflow_outputs": []
+    },
+    "7": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+      "errors": null,
+      "id": 7,
+      "input_connections": {
+        "experiment_schemes|infile_estimator": {
+          "id": 6,
+          "output_name": "outfile"
+        },
+        "input_options|infile1": {
+          "id": 0,
+          "output_name": "output"
+        },
+        "input_options|infile2": {
+          "id": 5,
+          "output_name": "outfile"
+        }
+      },
+      "inputs": [],
+      "label": null,
+      "name": "Deep learning training and evaluation",
+      "outputs": [
+        {
+          "name": "outfile_result",
+          "type": "tabular"
+        },
+        {
+          "name": "outfile_object",
+          "type": "zip"
+        },
+        {
+          "name": "outfile_weights",
+          "type": "h5"
+        }
+      ],
+      "position": {
+        "left": 450,
+        "top": 10
+      },
+      "post_job_actions": {},
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/1.0.8.3",
+      "tool_shed_repository": {
+        "changeset_revision": "785dd890e27d",
+        "name": "keras_train_and_eval",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"experiment_schemes\": {\"selected_exp_scheme\": \"train_val\", \"__current_case__\": 0, \"infile_estimator\": null, \"hyperparams_swapping\": {\"infile_params\": null, \"param_set\": []}, \"test_split\": {\"split_algos\": {\"shuffle\": \"simple\", \"__current_case__\": 1, \"test_size\": \"0.2\", \"random_state\": null}}, \"metrics\": {\"scoring\": {\"primary_scoring\": \"default\", \"__current_case__\": 0}}}, \"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": "1.0.8.3",
+      "type": "tool",
+      "uuid": "bb92ab0c-7b0c-4f3d-a53c-b1227265ec85",
+      "workflow_outputs": []
+    },
+    "8": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+      "errors": null,
+      "id": 8,
+      "input_connections": {
+        "infile_estimator": {
+          "id": 7,
+          "output_name": "outfile_object"
+        },
+        "infile_weights": {
+          "id": 7,
+          "output_name": "outfile_weights"
+        },
+        "input_options|infile1": {
+          "id": 2,
+          "output_name": "output"
+        }
+      },
+      "inputs": [],
+      "label": null,
+      "name": "Model Prediction",
+      "outputs": [
+        {
+          "name": "outfile_predict",
+          "type": "tabular"
+        }
+      ],
+      "position": {
+        "left": 670,
+        "top": 10
+      },
+      "post_job_actions": {},
+      "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/model_prediction/model_prediction/1.0.8.3",
+      "tool_shed_repository": {
+        "changeset_revision": "22f9cbcf1582",
+        "name": "model_prediction",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"infile_estimator\": null, \"infile_weights\": 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": "1.0.8.3",
+      "type": "tool",
+      "uuid": "0ee70cec-d22c-41d3-abf4-541d8f81df6d",
+      "workflow_outputs": []
+    },
+    "9": {
+      "annotation": "",
+      "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/ml_visualization_ex/ml_visualization_ex/1.0.8.3",
+      "errors": null,
+      "id": 9,
+      "input_connections": {
+        "plotting_selection|infile_predicted": {
+          "id": 8,
+          "output_name": "outfile_predict"
+        },
+        "plotting_selection|infile_true": {
+          "id": 3,
+          "output_name": "output"
+        }
+      },
+      "inputs": [],
+      "label": null,
+      "name": "Machine Learning Visualization Extension",
+      "outputs": [
+        {
+          "name": "output",
+          "type": "html"
+        }
+      ],
+      "position": {
+        "left": 890,
+        "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": "14bd6d59650d",
+        "name": "ml_visualization_ex",
+        "owner": "bgruening",
+        "tool_shed": "toolshed.g2.bx.psu.edu"
+      },
+      "tool_state": "{\"__input_ext\": \"input\", \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.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": "1.0.8.3",
+      "type": "tool",
+      "uuid": "d52fba8b-9eca-4fa8-af85-3a17ddd9530c",
+      "workflow_outputs": []
+    }
+  },
+  "tags": [
+    "statistics"
+  ],
+  "uuid": "dd391259-c91b-43a0-af66-25d1df37d832",
+  "version": 0
+}