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PyCaret - LORIS Tutorial #5539

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3dd4473
Loris tutorial start
paulocilasjr Oct 18, 2024
94cce58
first stab of the tutorial
paulocilasjr Oct 19, 2024
29a9796
new sections and images
paulocilasjr Oct 19, 2024
d644039
tutorial building
paulocilasjr Oct 21, 2024
cc413c7
test model input
paulocilasjr Oct 22, 2024
28fb2e8
report block added
paulocilasjr Oct 25, 2024
682a88a
tutorial changes
paulocilasjr Oct 28, 2024
64730ff
Merge branch 'galaxyproject:main' into loris_tutorial
paulocilasjr Oct 28, 2024
daf67b0
finished reports tabs
paulocilasjr Oct 31, 2024
a6e4887
changes
paulocilasjr Nov 2, 2024
1650a3d
update
paulocilasjr Nov 5, 2024
335f4f4
Merge pull request #2 from paulocilasjr/loris_tutorial
paulocilasjr Nov 7, 2024
5a0d1ba
Model comparison section
paulocilasjr Nov 11, 2024
f9a6ed1
tutorial progress
paulocilasjr Nov 13, 2024
f9a7bda
conclusions added
paulocilasjr Nov 13, 2024
3dd2f35
tutorial.md finished
paulocilasjr Nov 14, 2024
a964e73
tutorial finalized
paulocilasjr Nov 14, 2024
7ee04e4
Merge branch 'galaxyproject:main' into main
paulocilasjr Nov 14, 2024
37f52fc
Create Gemfile
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Create Gemfile.lock
paulocilasjr Nov 14, 2024
6649fb3
fix_tests-yml
paulocilasjr Nov 20, 2024
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Merge branch 'main' of github.com:paulocilasjr/training-material
paulocilasjr Nov 20, 2024
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fix-Labels
paulocilasjr Nov 20, 2024
8b2cd38
Merge branch 'galaxyproject:main' into main
paulocilasjr Nov 21, 2024
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fix - remove spaces
paulocilasjr Nov 21, 2024
e136884
fix test and tool ID
paulocilasjr Nov 21, 2024
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fix test identation
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Merge branch 'galaxyproject:main' into main
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Merge branch 'main' into main
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Merge branch 'main' into main
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2 changes: 2 additions & 0 deletions topics/statistics/tutorials/loris_model/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Tutorial_Galaxy-Pycaret
A galaxy tutorial to crete and run a logistic regression classifier with LORIS dataset (Chang et al., 2024)
23 changes: 23 additions & 0 deletions topics/statistics/tutorials/loris_model/data-library.yaml
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@@ -0,0 +1,23 @@
---
destination:
type: library
name: GTN - Material
description: Galaxy Training Network Material
synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
items:
- name: New topic
description: Topic summary
items:
- name: LORIS LLR6 model build
items:
- name: 'DOI: 10.5281/zenodo.13885908'
description: latest
items:
- url: https://zenodo.org/api/records/13885908/files/Chowell_train_Response.tsv/content
src: url
ext: ''
info: https://zenodo.org/records/13885908
- url: https://zenodo.org/api/records/13885908/files/Chowell_test_Response.tsv/content
src: url
ext: ''
info: https://zenodo.org/records/13885908
3 changes: 3 additions & 0 deletions topics/statistics/tutorials/loris_model/faqs/index.md
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@@ -0,0 +1,3 @@
---
layout: faq-page
---
36 changes: 36 additions & 0 deletions topics/statistics/tutorials/loris_model/tutorial.bib
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@@ -0,0 +1,36 @@

# This is the bibliography file for your tutorial.
#
# To add bibliography (bibtex) entries here, follow these steps:
# 1) Find the DOI for the article you want to cite
# 2) Go to https://doi2bib.org and fill in the DOI
# 3) Copy the resulting bibtex entry into this file
#
# To cite the example below, in your tutorial.md file
# use {% cite Batut2018 %}
#
# If you want to cite an online resourse (website etc)
# you can use the 'online' format (see below)
#
# You can remove the examples below

@article{Chang2024,
title = {LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features},
volume = {5},
ISSN = {2662-1347},
url = {http://dx.doi.org/10.1038/s43018-024-00772-7},
DOI = {10.1038/s43018-024-00772-7},
number = {8},
journal = {Nature Cancer},
publisher = {Springer Science and Business Media LLC},
author = {Chang, Tian-Gen and Cao, Yingying and Sfreddo, Hannah J. and Dhruba, Saugato Rahman and Lee, Se-Hoon and Valero, Cristina and Yoo, Seong-Keun and Chowell, Diego and Morris, Luc G. T. and Ruppin, Eytan},
year = {2024},
month = jun,
pages = {1158–1175}
}
@online{gtn-website,
author = {GTN community},
title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
url = {https://training.galaxyproject.org},
urldate = {2021-03-24}
}
273 changes: 273 additions & 0 deletions topics/statistics/tutorials/loris_model/tutorial.md

Large diffs are not rendered by default.

3 changes: 3 additions & 0 deletions topics/statistics/tutorials/loris_model/workflows/index.md
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---
layout: workflow-list
---
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@@ -0,0 +1,19 @@
- doc: Test the PyCaret comparison workflow
job:
'chowell_train':
location: https://zenodo.org/records/13885908/files/Chowell_train_Response.tsv
class: File
filetype: .tsv
'chowell_test':
location: https://zenodo.org/records/13885908/files/Chowell_test_Response.tsv
class: File
filetype: .tsv
outputs:
comparison_result:
asserts:
has_text:
text: "Model Training Report"
model:
asserts:
has_text:
text: "pycaret.internal.pipeline"
176 changes: 176 additions & 0 deletions topics/statistics/tutorials/loris_model/workflows/main_workflow.ga
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@@ -0,0 +1,176 @@
{
"a_galaxy_workflow": "true",
"annotation": "Generates LORIS LLR6 model ",
"creator":[
{
"class":"Person",
"identifier":"https://orcid.org/0000-0002-4403-6684",
"name":"Paulo Cilas Morais Lyra Junior"
},
{
"class":"Person",
"identifier":"https://orcid.org/0009-0005-4322-3401",
"name":"Junhao Qiu"
},
{
"class":"Person",
"identifier":"https://orcid.org/0000-0002-4583-5226",
"name":"Jeremy Goecks"
}
],
"format-version":"0.1",
"license": "AGPL-3.0-or-later",
"name":"Ludwig - Image recognition model - MNIST",
"steps": {
"0": {
"annotation": "Chowell train cohort - 964 samples",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "Chowell_Train_Response.tsv"
}
],
"label": "Chowell_Train_Response.tsv",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 292.9513931274414,
"height": 82.46527862548828,
"left": 356.9618225097656,
"right": 556.9618377685547,
"top": 210.48611450195312,
"width": 200.00001525878906,
"x": 356.9618225097656,
"y": 210.48611450195312
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "53bffd14-f503-4c81-8eb2-e70c0cec0559",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "66a19810-a401-47b6-8983-98e3f5e8757e"
}
]
},
"1": {
"annotation": "Chowell test cohort - 515 samples",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "Chowell_Test_Response.tsv"
}
],
"label": "Chowell_Test_Response.tsv",
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 402.9513931274414,
"height": 82.46527862548828,
"left": 355.97222900390625,
"right": 555.9722442626953,
"top": 320.4861145019531,
"width": 200.00001525878906,
"x": 355.97222900390625,
"y": 320.4861145019531
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "176d36e8-a459-4f51-9cff-932952f07f2f",
"workflow_outputs": [
{
"label": null,
"output_name": "output",
"uuid": "2b5382f7-f9b6-4715-aaf7-87e27fbdf8c6"
}
]
},
"2": {
"annotation": "",
"content_id": "pycaret_tool",
"errors": null,
"id": 2,
"input_connections": {
"input_file": {
"id": 0,
"output_name": "output"
},
"test_file": {
"id": 1,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool PyCaret Model Comparison",
"name": "input_file"
},
{
"description": "runtime parameter for tool PyCaret Model Comparison",
"name": "test_file"
}
],
"label": null,
"name": "PyCaret Model Comparison",
"outputs": [
{
"name": "model",
"type": "data"
},
{
"name": "comparison_result",
"type": "html"
}
],
"position": {
"bottom": 507.48268127441406,
"height": 297.013916015625,
"left": 684.96533203125,
"right": 884.9653472900391,
"top": 210.46876525878906,
"width": 200.00001525878906,
"x": 684.96533203125,
"y": 210.46876525878906
},
"post_job_actions": {},
"tool_id": "pycaret_tool",
"tool_state": "{\"advanced_settings\": {\"customize_defaults\": \"false\", \"__current_case__\": 1}, \"input_file\": {\"__class__\": \"RuntimeValue\"}, \"model_selection\": {\"model_type\": \"regression\", \"__current_case__\": 1, \"regression_models\": null}, \"random_seed\": \"42\", \"target_feature\": \"\", \"test_file\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.3.2+0",
"type": "tool",
"uuid": "2a5e0015-457e-475f-97aa-72183a56af18",
"workflow_outputs": [
{
"label": "PyCaret Model Comparison best model on input dataset(s)",
"output_name": "model",
"uuid": "5925cd98-b856-4dc2-87ae-0b07f2844386"
},
{
"label": "PyCaret Model Comparison Comparison result on input dataset(s)",
"output_name": "comparison_result",
"uuid": "a292d802-b28f-4707-862c-5454e4ebb886"
}
]
}
},
"tags":[
"LORIS",
"LLR6_model",
"Chowell_train_test",
"Logistic_Regression_Model"
],
"uuid":"a59d72a3-a167-4f94-87ea-0e3e18df1d4c",
"version": 1
}