MaAslin2-Tutorial #5173
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| --- | ||||||
| destination: | ||||||
| type: library | ||||||
| name: GTN - Material | ||||||
| description: Galaxy Training Network Material | ||||||
| synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org | ||||||
| items: | ||||||
| - name: The new topic | ||||||
| description: Summary | ||||||
| items: | ||||||
| - name: Determining multivariable association between various meta’omic features | ||||||
| using MaAslin2l | ||||||
| items: | ||||||
| - name: 'DOI: 10.5281/zenodo.12614561' | ||||||
| description: latest | ||||||
| items: | ||||||
| - url: https://zenodo.org/api/records/12614561/files/HMP2_metadata.tsv/content | ||||||
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There was a problem hiding this comment. why is it resolved, It's still not correct ... ? There was a problem hiding this comment. I thought miss Shilteman made the last update about this exactly , I did not notice it was data-library.yaml file you were mentioning. I am extremely sorry for that. I will make the necessary changes. |
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| src: url | ||||||
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| info: https://zenodo.org/records/12614561 | ||||||
| - url: https://zenodo.org/api/records/12614561/files/HMP2_taxonomy.tsv/content | ||||||
| src: url | ||||||
| ext: auto | ||||||
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| info: https://zenodo.org/records/12614561 | ||||||
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| layout: faq-page | ||
| --- |
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| # 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 | ||
|
|
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| @article{Batut2018, | ||
| doi = {10.1016/j.cels.2018.05.012}, | ||
| url = {https://doi.org/10.1016/j.cels.2018.05.012}, | ||
| year = {2018}, | ||
| month = jun, | ||
| publisher = {Elsevier {BV}}, | ||
| volume = {6}, | ||
| number = {6}, | ||
| pages = {752--758.e1}, | ||
| author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and | ||
| Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton | ||
| and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and | ||
| Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and | ||
| Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and | ||
| Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and | ||
| Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning}, | ||
| title = {Community-Driven Data Analysis Training for Biology}, | ||
| journal = {Cell Systems} | ||
| } | ||
|
|
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| @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} | ||
|
There was a problem hiding this comment. our bibtex parser is failing to parse urldate key. I think we should support this in the future, but perhaps for now you can set the date in a note so that the tests don't fail, e.g.:
There was a problem hiding this comment. Thanks ! Will make the necessary changes :) |
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| } | ||
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| - doc: "Test outline for Workflow-constructed-from-history-'Determining-multivariable-association-between-various-meta\u2019\ | ||
| omic-features-using-MaAslin2" | ||
| job: | ||
| HMP2_taxonomy.tsv: | ||
| location: https://zenodo.org/records/12614561/files/HMP2_taxonomy.tsv | ||
| class: File | ||
| filetype: tabular | ||
| HMP2_metadata.tsv: | ||
| location: https://zenodo.org/records/12614561/files/HMP2_metadata.tsv | ||
| class: File | ||
| filetype: tabular | ||
| outputs: | ||
| significant_results: | ||
| asserts: | ||
| has_n_columns: | ||
| n: 9 | ||
|
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| { | ||||||
| "a_galaxy_workflow": "true", | ||||||
| "annotation": "", | ||||||
| "comments": [], | ||||||
| "format-version": "0.1", | ||||||
| "name": "Workflow constructed from history 'Determining multivariable association between various meta\u2019omic features using MaAslin2", | ||||||
|
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Suggested change
This way? There was a problem hiding this comment. I kept the omitted part just to differentiate a between the title of workflow file and tutorial file. If it doesn't cause any issue then I believe we should not change it. What are your thoughts on this ? @bgruening There was a problem hiding this comment. I don't see any reason why a workflow should be named 'construceted from history' There was a problem hiding this comment. Can you please remove the two workflows, starting with Workflow constructed from history ...` and only keep the main one with the correct title ? |
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| "steps": { | ||||||
| "0": { | ||||||
| "annotation": "", | ||||||
| "content_id": null, | ||||||
| "errors": null, | ||||||
| "id": 0, | ||||||
| "input_connections": {}, | ||||||
| "inputs": [ | ||||||
| { | ||||||
| "description": "", | ||||||
| "name": "HMP2_taxonomy.tsv" | ||||||
| } | ||||||
| ], | ||||||
| "label": "HMP2_taxonomy.tsv", | ||||||
| "name": "Input dataset", | ||||||
| "outputs": [], | ||||||
| "position": { | ||||||
| "left": 10, | ||||||
| "top": 10 | ||||||
| }, | ||||||
| "tool_id": null, | ||||||
| "tool_state": "{\"optional\": false, \"tag\": null}", | ||||||
| "tool_version": null, | ||||||
| "type": "data_input", | ||||||
| "uuid": "2f31b06f-1730-427d-b729-363d0e77a8cd", | ||||||
| "when": null, | ||||||
| "workflow_outputs": [] | ||||||
| }, | ||||||
| "1": { | ||||||
| "annotation": "", | ||||||
| "content_id": null, | ||||||
| "errors": null, | ||||||
| "id": 1, | ||||||
| "input_connections": {}, | ||||||
| "inputs": [ | ||||||
| { | ||||||
| "description": "", | ||||||
| "name": "HMP2_metadata.tsv" | ||||||
| } | ||||||
| ], | ||||||
| "label": "HMP2_metadata.tsv", | ||||||
| "name": "Input dataset", | ||||||
| "outputs": [], | ||||||
| "position": { | ||||||
| "left": 10, | ||||||
| "top": 130 | ||||||
| }, | ||||||
| "tool_id": null, | ||||||
| "tool_state": "{\"optional\": false, \"tag\": null}", | ||||||
| "tool_version": null, | ||||||
| "type": "data_input", | ||||||
| "uuid": "8f312ad3-13b5-4664-902f-93eb071a14ef", | ||||||
| "when": null, | ||||||
| "workflow_outputs": [] | ||||||
| }, | ||||||
| "2": { | ||||||
| "annotation": "", | ||||||
| "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maaslin2/maaslin2/1.16.0+galaxy0", | ||||||
| "errors": null, | ||||||
| "id": 2, | ||||||
| "input_connections": { | ||||||
| "input_data": { | ||||||
| "id": 0, | ||||||
| "output_name": "output" | ||||||
| }, | ||||||
| "input_metadata": { | ||||||
| "id": 1, | ||||||
| "output_name": "output" | ||||||
| } | ||||||
| }, | ||||||
| "inputs": [], | ||||||
| "label": null, | ||||||
| "name": "MaAsLin 2", | ||||||
| "outputs": [ | ||||||
| { | ||||||
| "name": "figures_pdfs", | ||||||
| "type": "input" | ||||||
| }, | ||||||
| { | ||||||
| "name": "archive_output", | ||||||
| "type": "zip" | ||||||
| }, | ||||||
| { | ||||||
| "name": "all_results", | ||||||
| "type": "tabular" | ||||||
| }, | ||||||
| { | ||||||
| "name": "significant_results", | ||||||
| "type": "tabular" | ||||||
| }, | ||||||
| { | ||||||
| "name": "residuals", | ||||||
| "type": "rdata" | ||||||
| }, | ||||||
| { | ||||||
| "name": "headmap", | ||||||
| "type": "pdf" | ||||||
| } | ||||||
| ], | ||||||
| "position": { | ||||||
| "left": 230, | ||||||
| "top": 10 | ||||||
| }, | ||||||
| "post_job_actions": {}, | ||||||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maaslin2/maaslin2/1.16.0+galaxy0", | ||||||
| "tool_shed_repository": { | ||||||
| "changeset_revision": "43ccbef89f1d", | ||||||
| "name": "maaslin2", | ||||||
| "owner": "iuc", | ||||||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||||||
| }, | ||||||
| "tool_state": "{\"__input_ext\": \"input\", \"additional_options\": {\"min_abundance\": \"0.0\", \"min_prevalence\": \"0.1\", \"max_significance\": \"0.25\", \"normalization\": \"TSS\", \"transform\": \"LOG\", \"analysis_method\": \"LM\", \"correction\": null, \"standardize\": true}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fixed_effects\": [\"3\", \"4\"], \"input_data\": null, \"input_metadata\": null, \"output\": {\"plot_heatmap\": true, \"heatmap_first_n\": \"50\", \"plot_scatter\": true, \"residuals_output\": true}, \"random_effects\": [\"5\"], \"reference\": \"diagnosis,CD\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | ||||||
| "tool_version": "1.16.0+galaxy0", | ||||||
| "type": "tool", | ||||||
| "uuid": "d213582b-bf65-4705-a09b-73466f5007c1", | ||||||
| "when": null, | ||||||
| "workflow_outputs": [] | ||||||
| } | ||||||
| }, | ||||||
| "tags": [], | ||||||
| "uuid": "8da7151e-1680-44c8-b9c2-6ce5e127338a", | ||||||
| "version": 1 | ||||||
| } | ||||||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,3 @@ | ||
| --- | ||
| layout: workflow-list | ||
| --- |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| {"a_galaxy_workflow": "true", "annotation": "", "comments": [], "format-version": "0.1", "name": "Workflow constructed from history 'Determining multivariable association between various meta\u2019omic features using MaAslin2", "steps": {"0": {"annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "", "name": "HMP2_taxonomy.tsv"}], "label": "HMP2_taxonomy.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 10, "top": 10}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "2f31b06f-1730-427d-b729-363d0e77a8cd", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [{"description": "", "name": "HMP2_metadata.tsv"}], "label": "HMP2_metadata.tsv", "name": "Input dataset", "outputs": [], "position": {"left": 10, "top": 130}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "8f312ad3-13b5-4664-902f-93eb071a14ef", "when": null, "workflow_outputs": []}, "2": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/maaslin2/maaslin2/1.16.0+galaxy0", "errors": null, "id": 2, "input_connections": {"input_data": {"id": 0, "output_name": "output"}, "input_metadata": {"id": 1, "output_name": "output"}}, "inputs": [], "label": null, "name": "MaAsLin 2", "outputs": [{"name": "figures_pdfs", "type": "input"}, {"name": "archive_output", "type": "zip"}, {"name": "all_results", "type": "tabular"}, {"name": "significant_results", "type": "tabular"}, {"name": "residuals", "type": "rdata"}, {"name": "headmap", "type": "pdf"}], "position": {"left": 230, "top": 10}, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/maaslin2/maaslin2/1.16.0+galaxy0", "tool_shed_repository": {"changeset_revision": "43ccbef89f1d", "name": "maaslin2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "tool_state": "{\"__input_ext\": \"input\", \"additional_options\": {\"min_abundance\": \"0.0\", \"min_prevalence\": \"0.1\", \"max_significance\": \"0.25\", \"normalization\": \"TSS\", \"transform\": \"LOG\", \"analysis_method\": \"LM\", \"correction\": null, \"standardize\": true}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"fixed_effects\": [\"3\", \"4\"], \"input_data\": null, \"input_metadata\": null, \"output\": {\"plot_heatmap\": true, \"heatmap_first_n\": \"50\", \"plot_scatter\": true, \"residuals_output\": true}, \"random_effects\": [\"5\"], \"reference\": \"diagnosis,CD\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.16.0+galaxy0", "type": "tool", "uuid": "d213582b-bf65-4705-a09b-73466f5007c1", "when": null, "workflow_outputs": []}}, "tags": [], "uuid": "8da7151e-1680-44c8-b9c2-6ce5e127338a", "version": 1} |
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