Draft: workflow4meatbolomics lab

communities/workflow4metabolomics/lab/CONTRIBUTORS

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+# If GitHub username, name and avatar will be fetched and displayed
+bgruening
+bernt-matthias
+DamienCode404
+eschen42
+ethevenot
+fgiacomoni
+hechth
+jfrancoismartin
+jsaintvanne
+Lain-inrae
+lecorguille
+llegregam
+ManonMartin
+melpetera
+mmonsoor
+mtremblayfr
+npaulhe
+pkrog
+yguitton

communities/workflow4metabolomics/lab/base.yml

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+# Request this as a webpage with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/galaxyproject/galaxy_codex/tree/main/communities/microgalaxy/base.yml
+
+# -----------------------------------------------------------------------------
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites
+
+# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!"
+site_name: France
+lab_name: Workflow4Metabolomics
+analysis_name: Metabolomics
+nationality: European
+
+# Used for rendering tool/workflow links. Trailing '/' will be removed.
+galaxy_base_url: https://workflow4metabolomics.usegalaxy.fr
+subdomain: workflow4metabolomics
+root_domain: usegalaxy.fr
+support_url: https://help.galaxyproject.org/
+general_support: https://galaxyproject.org/support/
+figure_workflow4metabolomics_url: https://ifb-elixirfr.gitlab.io/usegalaxy-fr/welcome//workflow4metabolomics/images/workflow_w4m_HD.png
+
+# This will enable a feedback form on the webpage:
+# feedback_email: help@mygalaxy.org
+quota_request_url: https://community.france-bioinformatique.fr/c/workflow4metabolomics/10
+data_policy_url: https://ifb-elixirfr.gitlab.io/usegalaxy-fr/welcome//common/terms.html
+terms_url: https://ifb-elixirfr.gitlab.io/usegalaxy-fr/welcome//common/terms.html
+galaxy_help_url: https://help.galaxyproject.org
+galaxy_matrix_channel: https://matrix.to/#/#galaxyproject_Lobby:gitter.im
+european_server_matrix_channel: https://matrix.to/#/#usegalaxy-eu_Lobby:gitter.im
+
+help_links:
+  - title: Workflow4Metabolomics community forum
+    url: https://community.france-bioinformatique.fr/c/workflow4metabolomics/10
+  - title: General Galaxy support
+    url: https://galaxyproject.org/support/
+  - title: General Galaxy help forum
+    url: https://help.galaxyproject.org
+  - title: Galaxy Training Community chat
+    url: https://matrix.to/#/#Galaxy-Training-Network_Lobby:gitter.im
+
+intro_extra_md: ""
+conclusion_extra_md: ""
+
+# -----------------------------------------------------------------------------
+# Custom content relative to this file URL
+
+header_logo: static/w4m-lab-logo.png
+custom_css: static/custom.css
+intro_md: templates/intro.html
+conclusion_md: templates/conclusion.html
+footer_md: templates/footer.html
+
+
+# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
+# Either:
+#   1. Relative to this file URL
+#   2. Full URL to fetch globally centralized content
+sections:
+  - sections/1_data_import_and_preparation.yml
+  - sections/2_LCMS.yml
+  - sections/3_GCMS.yml
+  - sections/4_FIAMS.yml
+  - sections/5_NMR.yml
+  - sections/9_citations.yml
+
+# -----------------------------------------------------------------------------

communities/workflow4metabolomics/lab/sections/1_data_import_and_preparation.yml

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+id: data
+title: Getting started
+tabs:
+  - id: data-import
+    title: Data import
+    heading_md: >
+      Tools that allow for data import. 
+    content:
+      - title_md: Import data to Galaxy
+        description_md: >
+          Standard upload of data to Galaxy, from your computer or from the web.
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+        button_tip: Upload Data
+      - title_md:  Metabolights downloader
+        description_md: >
+          Import public and private MetaboLights studies
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fprog%2Fmtblsdwnld%2Fmtbls-dwnld"
+        button_tip: Metabolights downloader
+      - title_md:   Wishart bank downloader
+        description_md: >
+          Get a specific metabolite bank (as Urine, Serum...) from Wishart web portal.
+        button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Ffgiacomoni%2Fdownloader_bank_hmdb%2Fdownloader_bank_hmdb"
+        button_tip: Wishart bank downloader
+      - title_md:   HMDB MS search
+        description_md: >
+          Search by masses on HMDB v5 online LCMS bank
+        button_link: "{{ galaxy_base_url }}/tool_runner?toolshed.g2.bx.psu.edu%2Frepos%2Ffgiacomoni%2Fhmdb_ms_search%2Fwsdl_hmdb"
+        button_tip: HMDB MS search
+
+
+  - id: learning-pathways
+    title: Learning pathways 101
+    heading_md: >
+       Connected tutorials to train you to perform metabolomics data analysis.
+    content:
+      - title_md: Introduction to Galaxy
+        description_md: >
+          What is Galaxy?
+        button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/introduction/slides.html
+        button_tip: Open Learning Pathway
+        button_icon: view
+      - title_md: Galaxy Basics for everyone
+        description_md: >
+          This practical aims at familiarizing you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. 
+        button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
+        button_tip: Open Learning Pathway
+        button_icon: run
+      - title_md: Introduction to Metabolomics
+        description_md: >
+          The presentation will introduce you to the field of metabolomics, its applications, and the tools available in Galaxy for metabolomics data analysis.
+        button_link: https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/introduction/slides.html
+        button_tip: Open Learning Pathway
+        button_icon: view
+
+

communities/workflow4metabolomics/lab/sections/2_LCMS.yml

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+id: lcms
+title: LC/MS data analysis
+tabs:
+- id: overview
+  title: Overview
+  heading_md: ""
+- id: workflows
+  title: Workflows
+  heading_md: ""
+  content:
+    - title_md: "Mass spectrometry: LC-MS data processing"
+      description_md: >
+        This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).
+      button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=677'
+      button_tip: Import workflow
+      button_icon: run
+- id: tutorials
+  title: Tutorials
+  heading_md: Tutorials to train you to perform LC/MS data analysis
+  content:
+  - title_md: "Mass spectrometry: LC-MS preprocessing with XCMS - slides"
+    description_md: >
+      The slides will guide you through the steps of processing LC-MS data in Galaxy, including data import, quality control, and feature detection.
+    button_link: 
+      https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/slides.html
+    button_tip: View slides
+    button_icon: view
+  - title_md: "Mass spectrometry: LC-MS preprocessing with XCMS"
+    description_md: >
+      This tutorial will guide you through the steps of processing LC-MS data in Galaxy, including data import, quality control, and feature detection.
+    button_link: 
+      https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html
+    button_tip: View tutorial
+    button_icon: tutorial
+  - title_md: "Mass spectrometry: LC-MS data processing"
+    description_md: >
+      After the pre-processing step, what you have at your disposal is a list of ions (hereafter in the form of a “variableMetadata” file) and the corresponding intensities (“dataMatrix” file).
+      What you may want now is to get some relevant information from your tables. However, your data may not be suitable yet for statistical analysis.
+      What should you do to ensure the quality of your tables? This tutorial will show you what the usual quality steps are.
+    button_link: 
+      https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html
+    button_tip: View tutorial
+    button_icon: tutorial
+  - title_md: "Mass spectrometry: LC-MS analysis"
+    description_md: >
+      This tutorial explains the main steps involved in untargeted LC-MS data processing for metabolomic analysis, and shows how to conduct metabolomic data analysis from preprocessing to annotation using Galaxy.
+    button_link: 
+      https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html
+    button_tip: View tutorial
+    button_icon: tutorial
+

communities/workflow4metabolomics/lab/sections/3_GCMS.yml

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+id: gcms
+title: GC/MS data analysis
+tabs:
+- id: overview
+  title: Overview
+  heading_md: ""
+- id: workflows
+  title: Workflows
+  heading_md: ""
+  content:
+    - title_md: "GC/MS metaMS data processing"
+      description_md: >
+        This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.
+      button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=680'
+      button_tip: Import workflow
+      button_icon: run
+- id: tutorials
+  title: Tutorials
+  heading_md: Tutorials to train you to perform LC/MS data analysis
+  content:
+  - title_md: "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)"
+    description_md: >
+      This tutorial covers the main steps of gas chromatography-mass spectrometry (GC-MS) data processing for metabolomic analysis.
+    button_link: 
+      https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html
+    button_tip: View slides
+    button_icon: tutorial

communities/workflow4metabolomics/lab/sections/4_FIAMS.yml

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+id: fiams
+title: FIA/MS data analysis
+tabs:
+- id: overview
+  title: Overview
+  heading_md: ""
+

communities/workflow4metabolomics/lab/sections/5_NMR.yml

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+id: nmr
+title: NMR data analysis
+tabs:
+- id: overview
+  title: Overview
+  heading_md: ""
+

communities/workflow4metabolomics/lab/sections/9_citations.yml

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+id: citations
+title: Cite Us and Acknowledgements
+tabs:
+  - id: citations
+    title: Cite Us
+    heading_md: >
+      Please cite the following papers when using this tool:
+    content:
+      - title_md: Galaxy Project Primary Publication
+        description_md: >
+          The Galaxy Community. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024;, gkae410, https://doi.org/10.1093/nar/gkae410
+        button_link: "https://doi.org/10.1093/nar/gkae410"
+        button_tip: Access paper
+        button_icon: view
+      - title_md: "Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics"
+        description_md: >
+          Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics. doi:10.1093/bioinformatics/btu813
+        button_link: "https://doi.org/10.1093/bioinformatics/btu813"
+        button_tip: Access paper
+        button_icon: view
+      - title_md: Create, Run, Share, Publish, and Reference Your LC–MS, FIA–MS, GC–MS, and NMR Data Analysis Workflows with the Workflow4Metabolomics 3.0 Galaxy Online Infrastructure for Metabolomics.
+        description_md: >
+          Guitton, Yann, Marie Tremblay-Franco, Gildas Le Corguillé, Jean-François Martin, Mélanie Pétéra, Pierrick Roger-Mele, Alexis Delabrière, et al. 2017. “Create, Run, Share, Publish, and Reference Your LC–MS, FIA–MS, GC–MS, and NMR Data Analysis Workflows with the Workflow4Metabolomics 3.0 Galaxy Online Infrastructure for Metabolomics.” The International Journal of Biochemistry & Cell Biology 93: 89–101. doi.org/10.1016/j.biocel.2017.07.002
+        button_link: "https://doi.org/10.1016/j.biocel.2017.07.002"
+        button_tip: Access paper
+        button_icon: view
+  - id: acknowledgements
+    title: Acknowledgements
+    heading_md: >
+      Acknowledgements for the Workflow4Metabolomics supports when using this tool
+    content:
+      - title_md: "IFB Core Cluster: RENABI and MUDIS4LS funding"
+        description_md: >
+          We thank the IFB Core Cluster computing resource which has benefited from State aid managed by the Agence Nationale de la Recherche under the France 2030 programme for the Institut Français de Bioinformatique (IFB), founded by the Programme d'Investissements d'Avenir, number ANR-11-INBS-0013, as well as structuring equipment for research / EQUIPEX+ bearing the reference ANR-21-ESRE-0048.
+      - title_md: MetaboHub
+        description_md: >
+          We thank the Workflow4Metabolomics project, which is part of the French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr) and funded by the ANR (MetaboHUB-ANR-11-INBS-0010).
+  - id: funders
+    title: Funders
+    heading_md: >
+      Funders for the Workflow4Metabolomics project
+    content:
+      - title_md: "France 2030"
+        description_md: >
+          The [IFB (French Institute of Bioinformatics)](https://www.france-bioinformatique.fr/en/home/) and [MetaboHub](https://www.metabohub.fr/home.html) are supported by the France 2030 programme.
+      - title_md: "Brittany / Bretagne Region"
+        description_md: >
+          The ABiMS IFB platform is supported by the Brittany / Bretagne Region via [BioGenouest](https://www.biogenouest.org/en/).
+      - title_md: "Auvergne-Rhône-Alpes Region"
+        description_md: >
+          The PEFM platform is supported by the Auvergne-Rhône-Alpes Region.
+  - id: affiliations
+    title: Affiliations
+    heading_md: >
+      Affiliations of the Workflow4Metabolomics contributors' teams
+    content:
+      - title_md: "[CNRS - French National Centre for Scientific Research](https://www.cnrs.fr/en)"
+        description_md: >
+          Teams:
+          <ul>
+              <li>[IFB Core](https://www.france-bioinformatique.fr/en/organisation-governance/operational-cells/hub-ifb-core/) - Ivry-sur-Seine - France</li>
+              <li>[ABiMS](https://www.abims.fr/) (IFB) - [Station Biologique de Roscoff](https://www.sb-roscoff.fr/en), France</li>
+          </ul>
+      - title_md: "[INRAE - National Institute of Agricultural Research](https://www.inrae.fr/en)"
+        description_md: >
+          <ul>
+              <li>PEFM (MetaboHub) - Clermont-Ferrand, France</li>
+              <li>MetaToul-AXIOM (MetaboHub), Toxalim - Toulouse, France</li>
+              <li>[LABERCA](https://www.laberca.fr/) (Laboratoire d’Etude des Résidus et Contaminants dans les Aliments), ONIRIS (MetaboHub) - Nantes, France</li>
+          </ul>
+      - title_md: "[CEA - French Alternative Energies and Atomic Energy Commission](https://www.cea.fr/english)"
+        description_md: >
+          Team:
+          <ul>
+            <li>[LIST Laboratory for Data Analysis and Smart Systems](https://list.cea.fr/en/) (MetaboHub) - Saclay, France</li>
+          </ul>
+      - title_md: "[Université Libre de Bruxelles](https://www.ulb.be/en)"
+        description_md: >
+          <ul>
+              <li>[RD3 - Pharmacognosy, Bioanalysis & Drug Discovery Unit](https://pharmacie.ulb.be/version-francaise/la-recherche/les-unites-de-recherche/pharmacognosie-bioanalyse-et-medicaments-pbm/pharmacognosie-bioanalyse-et-medicaments-pbm) - Brussels, Belgium</li>
+          </ul>
+      - title_md: "[Sorbonne Université](https://www.sorbonne-universite.fr/en)"
+        description_md: >
+          <ul>
+              <li>[ABiMS](https://www.abims.fr/) (IFB) - [Station Biologique de Roscoff](https://www.sb-roscoff.fr/en), France</li>
+          </ul>
+      - title_md: "[University of Birmingham](https://www.birmingham.ac.uk)"
+        description_md: >
+          <ul>
+            <li>[Data Science and Computational Metabolomics](https://www.birmingham.ac.uk) - Birmingham, UK</li>
+          </ul>
+      - title_md: "[Masaryk University](https://www.muni.cz/en)"
+        description_md: >
+          <ul>
+              <li>[RECETOX](https://www.recetox.muni.cz/en) - Brno, Czech Republic</li>
+          </ul>

communities/workflow4metabolomics/lab/static/custom.css

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+#whatIsThisPage {
+  position: absolute;
+  top: 135px;
+  right: calc(50vw - 500px);
+}
+
+@media (max-width: 1070px) {
+  #whatIsThisPage {
+    right: 2rem;
+  }
+}
+@media (max-width: 992px) {
+  #whatIsThisPage {
+    top: 95px;
+  }
+}
+@media (max-width: 730px) {
+  #whatIsThisPage {
+    top: 2rem;
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communities/workflow4metabolomics/lab/templates/footer.html

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+<section class="my-5" id="tagline">
+
+    <div class="container">
+      <h5>Hosted by:</h5>
+      <div class="row align-items-center">
+        <div class="col-sm">
+          <a href="https://www.france-bioinformatique.fr/en/ifb-core-cluster/" target="_blank"><center><img src="https://www.france-bioinformatique.fr/wp-content/uploads/logo-ifb-couleur.svg" style="width:150px;" /></center></a>
+        </div>
+        <div class="col-sm">
+          <a href="https://elixir-europe.org/about-us/who-we-are/nodes/france" target="_blank"><center><img src="https://elixir-europe.org/sites/default/files/elixir_node_france_0.png" style="width:150px;" /></center></a>
+        </div>
+        <div class="col-sm">
+          <a href="https://www.economie.gouv.fr/france-2030" target="_blank"><center><img src="https://www.info.gouv.fr/upload/media/organization/0001/01/sites_default_files_contenu_illustration_2022_03_logotype-rouge-bleu.jpg" style="width:150px;" /></center></a>
+        </div>
+    </div>
+
+</section>