MaAslin2-Tutorial

CONTRIBUTORS.yaml

@@ -1858,7 +1858,11 @@ r1corre:
     twitter: r1corre
     orcid: 0000-0001-6354-2278
     joined: 2019-04
-
+
+renu-pal:
+    name: Renu Pal
+    joined: 2024-07
+
 rikeshi:
     name: Erik Schill
     joined: 2021-05

topics/microbiome/tutorials/multivariable-association/data-library.yaml

@@ -0,0 +1,24 @@
+---
+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
+        src: url
+        ext: tabular
+        info: https://zenodo.org/records/12614561
+      - url: https://zenodo.org/api/records/12614561/files/HMP2_taxonomy.tsv
+        src: url
+        ext: tabular
+        info: https://zenodo.org/records/12614561

topics/microbiome/tutorials/multivariable-association/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/microbiome/tutorials/multivariable-association/tutorial.bib

@@ -0,0 +1,42 @@
+
+# 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{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}
+}
+
+@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}
+}

topics/microbiome/tutorials/multivariable-association/workflows/Workflow-constructed-from-history-'Determining-multivariable-association-between-various-meta’omic-features-using-MaAslin2-tests.yml

@@ -0,0 +1,17 @@
+- 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
+

topics/microbiome/tutorials/multivariable-association/workflows/Workflow-constructed-from-history-'Determining-multivariable-association-between-various-meta’omic-features-using-MaAslin2.ga

@@ -0,0 +1,129 @@
+{
+    "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
+}

topics/microbiome/tutorials/multivariable-association/workflows/index.md

@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---

topics/microbiome/tutorials/multivariable-association/workflows/main_workflow.ga

@@ -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}