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workflow4metabolomics community automatic resources update #717
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| # Community subdomain/Lab |
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| {% load markdown %} | ||
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| <!-- <section class="my-5"> | ||
| {% if help_links %} | ||
| <h4 class="mb-3">{{ lab_name }} community support</h4> | ||
| <ul> | ||
| {% for link in help_links %} | ||
| <li> | ||
| <a href="{{ link.url }}" target="_blank">{{ link.title }}</a> | ||
| </li> | ||
| {% endfor %} | ||
| </ul> | ||
| {% endif %} | ||
| </section> | ||
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| <section> | ||
| <h4 class="mb-3">News and Events</h4> | ||
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| <div class="row justify-content-center"> | ||
| <div class="col"> | ||
| <iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe> | ||
| </div> | ||
| <div class="col"> | ||
| <iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe> | ||
| </div> | ||
| </div> | ||
| </section> --> | ||
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| {% if feedback_email %} | ||
| <section class="my-5"> | ||
| <h4 class="my-3">What do you think of the {{ lab_name }}?</h4> | ||
| <button | ||
| class="ga-btn" | ||
| data-bs-toggle="modal" | ||
| data-bs-target="#feedbackModal" | ||
| > | ||
| Give feedback | ||
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| </section> | ||
| {% endif %} | ||
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| <section class="my-5"> | ||
| <h4 class="mb-3">Cite Us</h4> | ||
| </section> | ||
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| <section class="my-5"> | ||
| If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage. | ||
| <!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>--> | ||
| </section> | ||
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| <section id="conclusionExtra"> | ||
| {{ conclusion_extra_md|safe }} | ||
| </section> |
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| <section class="my-5" id="tagline"> | ||
| <p> | ||
| Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community! | ||
| </p> | ||
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| <p> | ||
| #Here include an intro to your page, see the ex mple below from the microgalaxy community | ||
| # Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p> | ||
| <p> | ||
| <a | ||
| href="#" | ||
| data-bs-toggle="modal" | ||
| data-bs-target="#infoModal"> | ||
| How does this page relate to Galaxy {{ site_name }}? | ||
| </a> | ||
| </p> | ||
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| <div class="modal fade" id="infoModal" tabindex="-1"> | ||
| <div class="modal-dialog modal-lg"> | ||
| <div class="modal-content"> | ||
| <div class="modal-header"> | ||
| <h5 class="modal-title">Galaxy {{ site_name }}</h5> | ||
| <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button> | ||
| </div> | ||
| <div class="modal-body"> | ||
| <p> | ||
| This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website. | ||
| </p> | ||
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| <p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p> | ||
| <p><a class="ga-btn" href="{{support}}">Galaxy {{ site_name }} support</a></p> | ||
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| <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button> | ||
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| </div> | ||
| </div> | ||
| </div> | ||
| </section> | ||
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| id: tools | ||
| title: Community curated tools | ||
| tabs: [] |
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communities/workflow4metabolomics/lab/sections/3_workflows.yml
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communities/workflow4metabolomics/lab/sections/4_tutorials.yml
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| id: tutorials | ||
| title: Community curated tutorials | ||
| tabs: | ||
| - id: fair_data | ||
| title: FAIR Data | ||
| heading_md: 'Top 10 most visited tutorials for the Topic : FAIR Data. <br/> Visitors | ||
| : Number of unique visitors automatically calculated using Plausible.' | ||
| content: | ||
| - title_md: "DataPLANT ARCs\n (Visitors: 1829116)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/dataplant-arcs/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "FAIR in a nutshell\n (Visitors: 1107)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "FAIR data management solutions\n (Visitors: 486)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Making clinical datasets FAIR\n (Visitors: 441)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "FAIRification of an RNAseq dataset\n (Visitors: 394)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-rna/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Persistent Identifiers\n (Visitors: 377)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-persistent-identifiers/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Exporting Workflow Run RO-Crates from Galaxy\n (Visitors: 374)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Metadata\n (Visitors: 324)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "FAIR and its Origins\n (Visitors: 236)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "FAIR Galaxy Training Material\n (Visitors: 233)" | ||
| description_md: Tutorial stored in FAIR Data, Workflows, and Research topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - id: introduction_to_galaxy_analyses | ||
| title: Introduction to Galaxy Analyses | ||
| heading_md: 'Top 10 most visited tutorials for the Topic : Introduction to Galaxy | ||
| Analyses. <br/> Visitors : Number of unique visitors automatically calculated | ||
| using Plausible.' | ||
| content: | ||
| - title_md: "Galaxy Basics for genomics\n (Visitors: 55998)" | ||
| description_md: Tutorial stored in Introduction to Galaxy Analyses topic on | ||
| the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Data Manipulation Olympics\n (Visitors: 7006)" | ||
| description_md: Tutorial stored in Introduction to Galaxy Analyses topic on | ||
| the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "How to reproduce published Galaxy analyses\n (Visitors: 2442)" | ||
| description_md: Tutorial stored in Introduction to Galaxy Analyses topic on | ||
| the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Best Practices for Citing Galaxy\n (Visitors: 367)" | ||
| description_md: Tutorial stored in Introduction to Galaxy Analyses topic on | ||
| the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Introduction to Galaxy as an RDM platform\n (Visitors: 365)" | ||
| description_md: Tutorial stored in Introduction to Galaxy Analyses topic on | ||
| the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - id: metabolomics | ||
| title: Metabolomics | ||
| heading_md: 'Top 10 most visited tutorials for the Topic : Metabolomics. <br/> Visitors | ||
| : Number of unique visitors automatically calculated using Plausible.' | ||
| content: | ||
| - title_md: "Mass spectrometry: LC-MS preprocessing with XCMS\n (Visitors: 3995038)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Predicting EI+ mass spectra with QCxMS\n (Visitors: 1867817)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry: LC-MS analysis\n (Visitors: 14099)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry: LC-MS data processing\n (Visitors: 3455)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry imaging: Examining the spatial distribution of analytes\n\ | ||
| \ (Visitors: 3431)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, | ||
| and matchms)\n (Visitors: 3313)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry imaging: Finding differential analytes\n (Visitors: | ||
| 2250)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Mass spectrometry: GC-MS analysis with the metaMS package\n (Visitors: | ||
| 1988)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Molecular formula assignment and mass recalibration with MFAssignR | ||
| package\n (Visitors: 348)" | ||
| description_md: Tutorial stored in Metabolomics topic on the Galaxy Training | ||
| Network and covering topics related to Metabolomics | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - id: using_galaxy_and_managing_your_data | ||
| title: Using Galaxy and Managing your Data | ||
| heading_md: 'Top 10 most visited tutorials for the Topic : Using Galaxy and Managing | ||
| your Data. <br/> Visitors : Number of unique visitors automatically calculated | ||
| using Plausible.' | ||
| content: | ||
| - title_md: "Using dataset collections\n (Visitors: 17415)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Creating, Editing and Importing Galaxy Workflows\n (Visitors: 6557)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Understanding Galaxy history system\n (Visitors: 6073)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Rule Based Uploader\n (Visitors: 6040)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Extracting Workflows from Histories\n (Visitors: 3258)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Automating Galaxy workflows using the command line\n (Visitors: 3251)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Using Workflow Parameters\n (Visitors: 2160)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Workflow Reports\n (Visitors: 1026)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Rule Based Uploader: Advanced\n (Visitors: 935)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial | ||
| - title_md: "Annotate, prepare tests and publish Galaxy workflows in workflow registries\n\ | ||
| \ (Visitors: 475)" | ||
| description_md: Tutorial stored in Using Galaxy and Managing your Data topic | ||
| on the Galaxy Training Network and covering topics related to nan | ||
| button_link: | ||
| https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html | ||
| button_tip: View tutorial | ||
| button_icon: tutorial |
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Some sections require manual editing, such as this one. Please, check and ping us again for review once done
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We should have caught that in the review of your lab, you can do it now or in another PR