[Draft] Update for W4M - tool curation and labs update

_data/communities/workflow4metabolomics/curated_tools.yml

@@ -0,0 +1 @@
+../../../communities/workflow4metabolomics/resources/curated_tools.yml

communities/workflow4metabolomics/lab/base.yml

@@ -62,6 +62,8 @@ sections:
   - sections/3_GCMS.yml
   - sections/4_FIAMS.yml
   - sections/5_NMR.yml
-  - sections/9_citations.yml
+  - sections/6_support_and_help.yml
+  - sections/7_community.yml
+  - sections/8_citations.yml
 
 # -----------------------------------------------------------------------------

communities/workflow4metabolomics/lab/sections/6_support_and_help.yml

@@ -0,0 +1,55 @@
+id: support
+title: Support & Help
+tabs:
+  - id: help
+    title: Help
+    heading_md: >
+      You can request help through different channels. If you think your problem might help other users as well,
+      please post it in the Galaxy Help Forum. Please report tool bugs through our
+      [support channel]({{ support_url }})
+      and for specific questions feel free to reach out via the matrix chat.
+    content:
+      - title_md: Troubleshooting
+        description_md: >
+          Find specific advice for
+          {gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)
+          on the GTN.
+      - title_md: Galaxy Support
+        description_md: >
+          Any user of Galaxy {{ site_name }} can request support online!
+        button_md: Request support
+        button_link: "{{ support_url }}"
+        button_icon: help
+        button_tip: Request support
+#      - title_md: microGalaxy chat room
+#        description_md: >
+#          Chat with members of the microGalaxy community on Matrix
+#        button_link: "{{ microgalaxy_matrix }}"
+#        button_md: Matrix channel
+#        button_icon: social
+#        button_tip: Join the chat
+
+  - id: faq
+    title: FAQ
+    content:
+      - title_md: How can I increase my storage quota?
+        description_md: >
+          Please submit a quota request if your Galaxy  account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
+        button_md: Request
+        button_link: "{{ quota_request_url }}"
+        button_tip: Request quota
+        button_icon: help
+      - title_md: Can I upload sensitive data?
+        description_md: >
+          No, please do not upload personal or sensitive, such as human health or clinical data. Please see our
+          [Privacy Policy]({{ data_policy_url }})
+          page for definitions of sensitive and health-related information.
+
+          Please also make sure you have read our
+          [Terms of Service]({{ terms_url }}),
+          which covers hosting and analysis of research data.
+      - title_md: Is my data private?
+        description_md: >
+          Please read our
+          [Privacy Policy]({{ data_policy_url }})
+          for information on your personal data and any data that you upload.

communities/workflow4metabolomics/lab/sections/7_community.yml

@@ -0,0 +1,67 @@
+id: community
+title: Community
+tabs:
+  - id: participate
+    title: Participate
+    content:
+      - title_md: Join our community!
+        description_md: >
+          This Galaxy space is the result of hard, collaborative work by many contributors.
+#          It is maintained by the microGalaxy Community of Practice.
+#          This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier.
+#          Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)!
+#      - title_md: Chat with others!
+#        description_md: >
+#          Use our matrix channel to chat with others from microGalaxy community
+#        button_link: "{{ microgalaxy_matrix }}"
+#        button_md: 
+#        button_tip: Visit microGalaxy
+#        button_icon: social
+
+  - id: governance
+    title: How is the Galaxy Community organised?
+    heading_md: >
+      Learn about the
+      {gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN.
+    content: []
+
+  - id: links
+    title: Galaxy Community support links
+    content:
+      - title_md: "For general Galaxy support"
+        description_md: "General Galaxy support"
+        button_link: "{{ general_support }}"
+        button_tip: Galaxy Support
+        button_icon: help
+      - title_md: "General Help Forum"
+        description_md: "Access general Galaxy help"        
+        button_link: "{{ galaxy_help_url }}"
+        button_tip: Help forum
+        button_icon: help
+      - title_md: "Galaxy Training Network Slack Workspace"
+        description_md: "Join the GTN Slack community"
+        button_link: "{{ gtn_slack_url }}"
+        button_tip: Slack channel - Join the GTN Slack community.
+        button_icon: social
+      - title_md: "Galaxy Training Network Community Chat Room"
+        description_md: "Connect on the GTN Matrix chat"
+        button_link: "{{ gtn_matrix_channel }}"
+        button_tip: Matrix channel - Connect on the GTN Matrix chat.
+        button_icon: social
+#      - title_md: "microGalaxy User Community Chat Room"
+#        description_md: "Join the microGalaxy Matrix chat"
+#        button_link: "{{ microgalaxy_matrix }}"
+#        button_tip: Matrix channel - Join the microGalaxy Matrix chat.
+#        button_icon: social
+      - title_md: "General Galaxy Project Chat Room"
+        description_md: "Join the Galaxy project chat"
+        button_link: "{{ galaxy_matrix_channel }}"
+        button_tip: Matrix channel - Join the Galaxy project chat.
+        button_icon: social
+      - title_md: "European Galaxy Server Chat Room"
+        description_md: "Join the usegalaxy.eu chat"
+        button_link: "{{ european_server_matrix_channel }}"
+        button_tip: Matrix channel - Join the usegalaxy.eu chat.
+        button_icon: social
+        exclude_from:
+          - usegalaxy.org.au

communities/workflow4metabolomics/lab/sections/9_citations.yml → communities/workflow4metabolomics/lab/sections/8_citations.yml

@@ -12,6 +12,12 @@ tabs:
         button_link: "https://doi.org/10.1093/nar/gkae410"
         button_tip: Access paper
         button_icon: view
+      - title_md: Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data
+        description_md: >
+           Delporte, C., Tremblay-Franco, M., Guitton, Y., Canlet, C., Weber, R. J. M., Hecht, H., Price, E. J., Klánová, J., Joly, C., Dalle, C., Saint-Vanne, J., Thévenot, E., Schmitz, I., Chéreau, S., Dechaumet, S., Diémé, B., Giacomoni, F., Le Corguillé, G., Pétéra, M., & Souard, F. (2025). Workflow4Metabolomics (W4M): A user-friendly metabolomics platform for analysis of mass spectrometry and nuclear magnetic resonance data. Current Protocols, 5, e70095. doi: 10.1002/cpz1.70095
+        button_link: "https://doi.org/10.1002/cpz1.70095"
+        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
@@ -49,6 +55,9 @@ tabs:
       - title_md: "Auvergne-Rhône-Alpes Region"
         description_md: >
           The PEFM platform is supported by the Auvergne-Rhône-Alpes Region.
+      - title_md: "Ministry of Education, Youth and Sports of the Czech Republic"
+        description_md: >
+          This project is supported by the RECETOX Research Infrastructure (No LM2023069) financed by the Ministry of Education, Youth and Sports (MEYS) of the Czech Republic.
   - id: affiliations
     title: Affiliations
     heading_md: >
@@ -77,12 +86,12 @@ tabs:
       - 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>
+              <li>[RD3 - Pharmacognosy, Bioanalysis and 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>
+              <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: >
@@ -92,5 +101,5 @@ tabs:
       - title_md: "[Masaryk University](https://www.muni.cz/en)"
         description_md: >
           <ul>
-              <li>[RECETOX](https://www.recetox.muni.cz/en) - Brno, Czech Republic</li>
+              <li>[RECETOX, Faculty of Science, Masaryk University](https://www.recetox.muni.cz/en) - Brno, Czech Republic</li>
           </ul>

communities/workflow4metabolomics/lab/templates/footer.html

@@ -4,13 +4,16 @@
       <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>
+          <a href="https://www.france-bioinformatique.fr/en/ifb-core-cluster/" target="_blank"><center><img src="static/ifb-logo.png" 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>
+          <a href="https://www.economie.gouv.fr/france-2030" target="_blank"><center><img src="static/france2030-logo.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>
+          <a href="https://www.recetox.muni.cz/en" target="_blank"><center><img src="static/muni_recetox_sci.png" style="width:150px;" /></center></a>
+        </div>
+        <div class="col-sm">
+          <a href="https://elixir-europe.org/" target="_blank"><center><img src="static/ELIXIR_logo_standard.png" style="width:150px;" /></center></a>
         </div>
     </div>