diff --git a/.gitignore b/.gitignore index dd488489dc4505..9b9fdbac27c2a9 100644 --- a/.gitignore +++ b/.gitignore @@ -24,3 +24,4 @@ tool_test_output* plnmotmp*.json # Planemo output for workflow autoupdate tools.yml +api/** diff --git a/_includes/default-footer.html b/_includes/default-footer.html index 1b7a4471896149..e29cd1abbef163 100644 --- a/_includes/default-footer.html +++ b/_includes/default-footer.html @@ -2,38 +2,71 @@
-
+
+ GTN

- The Galaxy Training Network - provides researchers with online training materials, connects them with local trainers, and helps promoting FAIR and Open Science practices worldwide. All contributions are subject to the Galaxy Project Code of Conduct. + The GTN provides researchers with a free, open repository of online training + materials, with a focus on hands-on training that aims to be directly applicable for learners. + We aim to connect researchers and learners with local trainers, and events worldwide.

- The GTN infrastructure is licensed under MIT + We promote FAIR and Open Science practices worldwide, are committed to the accessibility of this platform and training for everyone.

+ +
+

- Revision {{ site.git_revision_short }}, built with Jekyll ({{ jekyll.version }} | {{ jekyll.environment }}) + About Us +

-
-
- {% if page.short_id %}

- Resource {% icon purl %}PURL: https://gxy.io/GTN:{{ page.short_id }} + Contact +

- {% endif %} +
+

- This Material: - {% if page.copyright %} - is {{ page.copyright }}. - {% endif %} - is licensed under - - {% if page.license %}{{ page.license }}{% else %}Creative Commons Attribution 4.0 International License{% endif %} - + Framework +

+
+
+ Page

- - {% icon github %} Edit on GitHub - +

diff --git a/_includes/schema-render.html b/_includes/schema-render.html index afdb217a8b4fcf..7d0f77452df4f5 100644 --- a/_includes/schema-render.html +++ b/_includes/schema-render.html @@ -5,7 +5,7 @@ {% if include.key == "=" %} Any key permitted {% else %} - {{ include.key }} + (Required) {{ include.key }} {% endif %} {% else %}
@@ -85,3 +84,59 @@

{{locale['references']| default: "References" }}

+ + + + + diff --git a/_plugins/snippet.rb b/_plugins/snippet.rb index a2b0994457d88f..bb065d78c6e3fe 100644 --- a/_plugins/snippet.rb +++ b/_plugins/snippet.rb @@ -80,7 +80,7 @@ def render(context) box_end = "\n{: .#{box_type}}" end end - y = x.gsub(/\A---(.|\n)*?---/, '') + y = x.split("\n---\n", 2).last # if y =~ /contribute/ # puts "=== step 1 ===\n#{y}\n\n" # end diff --git a/accessibility.md b/accessibility.md index 83f61c3506d862..4e1fa86667893b 100644 --- a/accessibility.md +++ b/accessibility.md @@ -7,6 +7,8 @@ title: GTN Accessibility The Galaxy Training Network is committed to making its content accessible to all learners, including those with disabilities. While we are a volunteer organisation, we are constantly working to ensure that our training materials are accessible to everyone, regardless of their abilities or background. We use a variety of accessibility features and tools, including alt text, closed captioning, and automated testing, to make our content accessible to all learners. +We aim for WCAG 2.0 AA compliance (AAA where possible), under the default theme and styling of the GTN. We are investigating our Section 508 compliance. + ### Accessibility Features #### Visual diff --git a/assets/css/main.scss b/assets/css/main.scss index c7cccde8317fde..de6d070ac4600e 100644 --- a/assets/css/main.scss +++ b/assets/css/main.scss @@ -445,7 +445,6 @@ div.language-diff .p { body > footer { margin-top: 5em; - text-align: center; } footer { @@ -486,7 +485,7 @@ nav.navbar { } a.navbar-brand { - padding-right: 0.5em; // the image seems to work poorly with parent size calculations. + padding-right: 2.5em; // the image seems to work poorly with parent size calculations. } // Text decoration not necessary for accessibility here. @@ -1655,9 +1654,13 @@ $btn-pink: var(--keypoints-color); padding: 0rem; } +ul.no-bullets { + list-style: none; + padding-inline-start: 0; +} ul.text-list, ol.text-list { - list-style: none; - padding-inline-start: 0; + list-style: none; + padding-inline-start: 0; li { display: inline; @@ -1880,6 +1883,20 @@ body[data-brightness="dark"] { img.invert-safe { filter: invert(1); } + + .modal-content { + button.close { + filter: invert(1); + } + } +} + +.modal-dialog { + border: 1px solid var(--border); + + .modal-content { + background: var(--color-background); + } } diff --git a/assets/css/themes.scss b/assets/css/themes.scss index 9156ce3c780399..04eaf8a373d247 100644 --- a/assets/css/themes.scss +++ b/assets/css/themes.scss @@ -151,7 +151,7 @@ body[data-theme="straya"] { --h1-theme-after: " 🦈 "; --h2-theme-before: " 🐨 "; --h2-theme-after: " 🐨 "; - --brand-color: #0d47a1; + --brand-color: #00843d; hr { height: 0.5em; diff --git a/bin/gtn.rb b/bin/gtn.rb index 0f6b6439d9273a..1de7f225e5e203 100644 --- a/bin/gtn.rb +++ b/bin/gtn.rb @@ -7,7 +7,7 @@ def automagic_loading(f) # Remove our documentation f.reject! { |k, v| k == 'description' and v.is_a?(String) } - f.reject! { |k| k == 'examples' } + f.reject! { |k| k == '_examples' } # Auto-replace CONTRIBUTORS in enums. f.each do |k, v| diff --git a/bin/schema-contributors.yaml b/bin/schema-contributors.yaml index b65da13b218fcc..0ecf767339915e 100644 --- a/bin/schema-contributors.yaml +++ b/bin/schema-contributors.yaml @@ -1,6 +1,6 @@ --- type: map -examples: | +_examples: | hexylena: name: Helena twitter: hexylena @@ -16,7 +16,7 @@ mapping: required: true description: | Your preferred name. If you prefer an alias or another name, this is welcome, it does not need to be your legal name. - examples: + _examples: - 张三 - Alice - Jane Doe @@ -27,25 +27,25 @@ mapping: pattern: /@/ description: | Your email address, if you wish to provide it. - examples: + _examples: - jane.doe@gmail.com twitter: type: str pattern: /[0-9a-zA-Z]+/ description: Your twitter handle, without the `@` - examples: + _examples: - gxytraining bluesky: type: str pattern: /[0-9a-zA-Z.]+/ description: Your bluesky handle - examples: + _examples: - gtn.bsky.social fediverse: type: str pattern: /^https:\/\/[0-9a-zA-Z.]+/@?[0-9a-zA-Z.]+$/ description: The URL to your fediverse profile - examples: + _examples: - http://genomic.social/@abretaud fediverse_flavor: type: str @@ -57,13 +57,13 @@ mapping: type: str description: | A short biography of yourself, if you wish to add additional details or context. - examples: + _examples: - Research at the [South African National Bioinformatics Institute](https://www.sanbi.ac.za/) matrix: type: str pattern: /[0-9a-zA-Z]+:.*/ description: Your matrix identifier and home server - examples: + _examples: - "hexylena:matrix.org" linkedin: type: str @@ -79,14 +79,14 @@ mapping: type: str pattern: /[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}/ description: Your identifier at orcid.org - examples: + _examples: - 0000-0001-9760-8992 joined: type: str required: true pattern: /[0-9]{4,}-[0-9]{2}/ description: The year and month in which you joined - examples: + _examples: - 2020-01 halloffame: type: str @@ -155,16 +155,16 @@ mapping: country: type: str description: The country you work in, ISO-3166-2 code. - examples: + _examples: - NL - DE lat: type: float description: Latitude in decimal numbers - examples: + _examples: - 4.12 lon: type: float description: Longitude in decimal numbers - examples: + _examples: - 55.0 diff --git a/bin/schema-event-external.yaml b/bin/schema-event-external.yaml index 0ccc4a3fc455fc..7fccd70f6377d8 100644 --- a/bin/schema-event-external.yaml +++ b/bin/schema-event-external.yaml @@ -18,14 +18,14 @@ mapping: required: true description: | Title of the event - examples: + _examples: - Smörgåsbord 2023 - MTS Basics Workshop contributions: required: true description: | List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial. - examples: | + _examples: | contributions: organisers: - shiltemann @@ -104,19 +104,19 @@ mapping: type: date description: | When the event starts - examples: + _examples: - 2024-04-01 date_end: type: date description: | When the event ends - examples: + _examples: - 2024-04-01 location: required: false description: | Physical location of the event, only required for in-person events - examples: | + _examples: | location: name: Zoom location: diff --git a/bin/schema-event.yaml b/bin/schema-event.yaml index 07a28bc7e47d48..f9364b3d0fbfd9 100644 --- a/bin/schema-event.yaml +++ b/bin/schema-event.yaml @@ -13,14 +13,14 @@ mapping: required: true description: | Title of the event - examples: + _examples: - Smörgåsbord 2023 - MTS Basics Workshop contributions: required: true description: | List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial. - examples: | + _examples: | contributions: organisers: - shiltemann @@ -106,38 +106,38 @@ mapping: - type: str description: | If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible. - examples: + _examples: - /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial cover-image: type: str pattern: /^\/.*(.png|.jpg|.jpeg)/ description: | link to a picture that will be used as the cover for the article - examples: + _examples: - "/assets/images/BYCOVID_logo_tagline.png" cover-image-alt: type: str description: | If a cover is provided, then alt text is Mandatory. - examples: + _examples: - "logo of by covid with subtitle reading beyond covid" date_start: type: date description: | When the event starts - examples: + _examples: - 2024-04-01 date_end: type: date description: | When the event ends - examples: + _examples: - 2024-04-01 location: required: false description: | Physical location of the event, only required for in-person events - examples: | + _examples: | location: name: Zoom location: @@ -173,13 +173,13 @@ mapping: pattern: /(free|\d+ [A-Z]{3})/ description: | Price of the event. If the event is free, use the word `free`. If there is a cost, use the currency and amount. - examples: + _examples: - free - 123 EUR - 456 USD audience: type: str - examples: + _examples: - This event is intended for PhD students interested in Genomics. A basic knowledge in R is useful but not required. contact_email: type: str @@ -311,6 +311,6 @@ mapping: required: true description: | A free form list of tags that are relevant for your tutorial. - examples: + _examples: - covid-19 - git-gat diff --git a/bin/schema-faq.yaml b/bin/schema-faq.yaml index a2ff99632b028b..4a6a601bac0177 100644 --- a/bin/schema-faq.yaml +++ b/bin/schema-faq.yaml @@ -13,7 +13,7 @@ mapping: required: true description: | Title of the FAQ - examples: + _examples: - How does the GTN implement the 'Ten simple rules for collaborative lesson development' - How can I give feedback? - Ways to use Galaxy @@ -22,7 +22,7 @@ mapping: required: false description: | A short, one line description to provide additional context of the FAQ - examples: + _examples: - Galaxy may have several reference genomes built-in, but you can also create your own. - Quickly learn what the identifiers are in any **BAM** dataset that is the result from mapping - Finding and Correcting Metadata @@ -31,7 +31,7 @@ mapping: required: false description: | A text key used for sorting related FAQs together in the visual interface for users. - examples: + _examples: - contributors - learners - features @@ -53,7 +53,7 @@ mapping: required: true description: | Who contributed to this FAQ - examples: + _examples: - shiltemann - hexylena sequence: @@ -68,6 +68,36 @@ mapping: - type: str description: | If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible. - examples: + _examples: - /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial + required_parameters: + type: map + mapping: + "=": + type: str + description: | + A list of parameters that are required to be set when invoking the FAQ, otherwise the FAQ will not render correctly (e.g. in the FAQ list!) + _examples: | + name: The name of the dataset + optional_parameters: + type: map + mapping: + "=": + type: str + description: | + Optional parameters that can enhance the experience of the learner if set correctly + _examples: | + format: the format they should change it to + examples: + type: map + mapping: + '=': + type: map + mapping: + '=': {type: str} + description: | + A list of _examples that can be used to illustrate the FAQ's invocation + _examples: | + A very basic included version: {} + A more complex example: {name: "Phages", format: "genbank"} --- diff --git a/bin/schema-funders.yaml b/bin/schema-funders.yaml index bcd8977c0abbad..3f01d1ca52142d 100644 --- a/bin/schema-funders.yaml +++ b/bin/schema-funders.yaml @@ -1,6 +1,6 @@ --- type: map -examples: | +_examples: | erasmusplus: name: Erasmus+ bio: We funded some of this work! @@ -15,32 +15,32 @@ mapping: required: true description: | The full name for the grant - examples: + _examples: - Gallantries: Bridging Training Communities in Life Science, Environment and Health short_name: type: str description: | A shorter name, as some grants love to stuff a lot of words into the title - examples: + _examples: - Gallantries email: type: str pattern: /@/ description: | Your email address, if you wish to provide it. - examples: + _examples: - jane.doe@gmail.com twitter: type: str pattern: /[0-9a-zA-Z]+/ description: Your twitter handle, without the `@` - examples: + _examples: - gxytraining fediverse: type: str pattern: /^https:\/\/[0-9a-zA-Z.]+/@?[0-9a-zA-Z.]+$/ description: The URL to your fediverse profile - examples: + _examples: - http://genomic.social/@abretaud fediverse_flavor: type: str @@ -52,13 +52,13 @@ mapping: type: str description: | A short biography of yourself, if you wish to add additional details or context. - examples: + _examples: - Research at the [South African National Bioinformatics Institute](https://www.sanbi.ac.za/) matrix: type: str pattern: /[0-9a-zA-Z]+:.*/ description: Your matrix identifier and home server - examples: + _examples: - "hexylena:matrix.org" linkedin: type: str @@ -71,25 +71,25 @@ mapping: type: str pattern: /[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}/ description: Your identifier at orcid.org - examples: + _examples: - 0000-0001-9760-8992 joined: type: str pattern: /[0-9]{4,}-[0-9]{2}/ description: The year and month in which you joined - examples: + _examples: - 2020-01 start_date: type: str pattern: /[0-9]{4,}-[0-9]{2}-[0-9]{2}/ description: The start date of the grant - examples: + _examples: - "2020-01-01" end_date: type: str pattern: /[0-9]{4,}-[0-9]{2}-[0-9]{2}/ description: The end date of the grant - examples: + _examples: - "2020-01-01" avatar: type: str @@ -102,12 +102,12 @@ mapping: funding_id: type: str description: The short identifier for your grant. - examples: + _examples: - 2020-1-NL01-KA203-064717 url: type: str description: associated webpage (NOTE, funders only!) - examples: + _examples: - "https://elixir-europe.org" funding_system: type: str @@ -119,10 +119,10 @@ mapping: funder_name: type: str description: A name for the agency providing the funding. - examples: + _examples: - Erasmus+ Programme funding_statement: type: str description: A short statement about the funder, markdown is supported. - examples: + _examples: - This project ([`2020-1-NL01-KA203-064717`](https://erasmus-plus.ec.europa.eu/projects/search/details/2020-1-NL01-KA203-064717)) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics. diff --git a/bin/schema-learning-pathway.yaml b/bin/schema-learning-pathway.yaml index 9a65fb2eddbd49..7852cf67dbd301 100644 --- a/bin/schema-learning-pathway.yaml +++ b/bin/schema-learning-pathway.yaml @@ -10,7 +10,7 @@ mapping: required: true description: | Title of the pathway - examples: + _examples: - Clustering in Machine Learning - Breve introducción a Galaxy - en español - Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools diff --git a/bin/schema-news.yaml b/bin/schema-news.yaml index b5b422b6db049c..94cd79e23635ba 100644 --- a/bin/schema-news.yaml +++ b/bin/schema-news.yaml @@ -11,7 +11,7 @@ mapping: required: true description: | Title of the news post - examples: + _examples: - 'BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More' - "New Tutorial Feature: Choose Your Own Tutorial" tags: @@ -21,7 +21,7 @@ mapping: required: true description: | A free form list of tags that are relevant for your tutorial. - examples: + _examples: - new topic - new tutorial - new feature @@ -38,14 +38,14 @@ mapping: - FUNDERS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. - examples: + _examples: - hexylena - shiltemann contributions: required: true description: | List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial. - examples: | + _examples: | contributions: authorship: - shiltemann @@ -125,13 +125,13 @@ mapping: type: str description: | link to a picture that will be used as the cover for the article - examples: + _examples: - "assets/images/BYCOVID_logo_tagline.png" coveralt: type: str description: | If a cover is provided, then alt text is Mandatory. - examples: + _examples: - "logo of by covid with subtitle reading beyond covid" abbreviations: type: map @@ -142,7 +142,7 @@ mapping: The expansion of the abbreviated term. description: | A dictionary of abbreviations and their expansions. - examples: | + _examples: | abbreviations: SQL: Structured Query Language API: Application Programming Interface @@ -152,19 +152,19 @@ mapping: - type: str description: | If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible. - examples: + _examples: - /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial tutorial: type: str description: | Include a link to a specific page as a call to action button at the bottom of the page. - examples: + _examples: - topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.html link: type: str description: | Basically an alias for tutorial, except requiring a full URL - examples: + _examples: - https://example.org external: type: bool diff --git a/bin/schema-organisations.yaml b/bin/schema-organisations.yaml index 23526bb5f2d80c..1f34176aacc146 100644 --- a/bin/schema-organisations.yaml +++ b/bin/schema-organisations.yaml @@ -1,6 +1,6 @@ --- type: map -examples: | +_examples: | elixir: name: ELIXIR bio: We contribute as an organisation! @@ -15,7 +15,7 @@ mapping: required: true description: | Your preferred name. If you prefer an alias or another name, this is welcome, it does not need to be your legal name. - examples: + _examples: - 张三 - Alice - Jane Doe @@ -26,19 +26,19 @@ mapping: pattern: /@/ description: | Your email address, if you wish to provide it. - examples: + _examples: - jane.doe@gmail.com twitter: type: str pattern: /[0-9a-zA-Z]+/ description: Your twitter handle, without the `@` - examples: + _examples: - gxytraining fediverse: type: str pattern: /^https:\/\/[0-9a-zA-Z.]+/@?[0-9a-zA-Z.]+$/ description: The URL to your fediverse profile - examples: + _examples: - http://genomic.social/@abretaud fediverse_flavor: type: str @@ -50,13 +50,13 @@ mapping: type: str description: | A short biography of yourself, if you wish to add additional details or context. - examples: + _examples: - Research at the [South African National Bioinformatics Institute](https://www.sanbi.ac.za/) matrix: type: str pattern: /[0-9a-zA-Z]+:.*/ description: Your matrix identifier and home server - examples: + _examples: - "hexylena:matrix.org" linkedin: type: str @@ -69,18 +69,18 @@ mapping: type: str pattern: /[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}/ description: Your identifier at orcid.org - examples: + _examples: - 0000-0001-9760-8992 joined: type: str pattern: /[0-9]{4,}-[0-9]{2}/ description: The year and month in which you joined - examples: + _examples: - 2020-01 avatar: type: str url: type: str description: associated webpage (NOTE, funders only!) - examples: + _examples: - "https://elixir-europe.org" diff --git a/bin/schema-quiz.yaml b/bin/schema-quiz.yaml index 413ea45a1be652..0f83386603a708 100644 --- a/bin/schema-quiz.yaml +++ b/bin/schema-quiz.yaml @@ -6,7 +6,7 @@ mapping: required: true description: | Title of the Quiz - examples: + _examples: - Diagnostic Assessment - SQL Basics Recap contributors: @@ -14,7 +14,7 @@ mapping: required: true description: | Who contributed to this FAQ - examples: + _examples: - shiltemann - hexylena sequence: @@ -35,7 +35,7 @@ mapping: required: true description: | The question title, displayed on the teacher and student screens simultaneously - examples: + _examples: - How you could collect information from learners at the beginning of a course or lesson and how you can use it? - What keyword do you use to retrieve data in SQL answers: @@ -44,7 +44,7 @@ mapping: The possible answers to the question you've asked. Consider including common wrong answers, or answers based on common mistakes to help students identify where they went wrong. - examples: + _examples: - OBTAIN - SELECT - RETRIEVE @@ -54,7 +54,7 @@ mapping: correct: type: any description: The correct answer, it MUST be part of the answers list. It can be a list of correct answers if it is a choose-many question - examples: + _examples: - SELECT - [A, B] timeout: @@ -64,7 +64,7 @@ mapping: image: type: str description: Path to an image, if you'd like to include one along with the question. Should be the full path starting with / - examples: + _examples: - /training-material/topics/data-science/images/carpentries-sql/sql-join-structure.svg live: type: bool diff --git a/bin/schema-slides.yaml b/bin/schema-slides.yaml index d4c703909fada9..b7e85411113e11 100644 --- a/bin/schema-slides.yaml +++ b/bin/schema-slides.yaml @@ -16,7 +16,7 @@ mapping: required: true description: | Title of the slides (it will appear on the slides and the topic listing) - examples: + _examples: - Introduction to CRISPR screen analysis - High Performance Computing for Pairwise Genome Comparison - Circos @@ -27,7 +27,7 @@ mapping: required: true description: | list of questions that will be addressed in the slides - examples: + _examples: - What is ATAC-Seq? - What are Galaxy Interactive Environments (GIEs)? - How to visualize your genome after automated annotations have been performed? @@ -44,7 +44,7 @@ mapping: - Compute (Skill) - multiple whole genome assemblies (Objective) - in such a way to develop big data processing skills (Result) - examples: + _examples: - Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis* - Explore Biodiversity data with taxonomic, temporal and geographical informations - Generate a DotPlot emulating the original paper using a different analysis tool @@ -58,7 +58,7 @@ mapping: of the slides. These should really be a key point, something that should stick in their mind; what you want them to take home from the slides. - examples: + _examples: - Pangeo is an inclusive community promoting open, reproducible and scalable science. - Balanced batches and replicates allow bioinformatic batch correction - Galaxy workflows can download images from the IDR, selecting specific channels, time points, z-stack positions and crop the image in different ways. @@ -69,7 +69,7 @@ mapping: pattern: /^topic_[0-9]+$/ description: | An edam ontology id that describes the resource - examples: + _examples: - topic_3173 video: type: bool @@ -87,14 +87,14 @@ mapping: - ORGANISATIONS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. - examples: + _examples: - hexylena - shiltemann contributions: required: true description: | List of slide contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial. - examples: | + _examples: | contributions: authorship: - shiltemann @@ -180,18 +180,18 @@ mapping: type: str description: | if the topic has [multiple subtopics defined](/training-material/topics/contributing/tutorials/create-new-topic/tutorial.html#adapt-the-metadata-for-your-topic), you can assign your tutorial to one of those subtopics here. Without this, the tutorial will appear in the "Other tutorials" section on the topic page. - examples: + _examples: - single-cell priority: type: int description: | This field allows ordering resources within the topic list. Learning resources with lower numbered priority come before those with higher numbers. - examples: 1 + _examples: 1 zenodo_link: type: str description: | link on Zenodo to the input data for the tutorial - examples: + _examples: - "https://zenodo.org/record/3706539" logo: type: str @@ -218,7 +218,7 @@ mapping: required: true description: | A free form list of tags that are relevant for your tutorial. - examples: + _examples: - covid-19 - git-gat translations: @@ -227,7 +227,7 @@ mapping: - type: str description: | If alternative translations of a material are available, then use this key to indicate which languages have been manually translated. - examples: + _examples: - en level: type: str @@ -248,7 +248,7 @@ mapping: - type: str description: | If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible. - examples: + _examples: - /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial lang: type: str @@ -275,7 +275,7 @@ mapping: type: float endOfSlidePause: type: float - examples: | + _examples: | voice: id: Lupe lang: es-US @@ -283,7 +283,7 @@ mapping: follow_up_training: type: seq description: list of resources that the reader of the material could follow at the end of the tutorial - examples: + _examples: - | type: internal topic_name: statistics @@ -330,7 +330,7 @@ mapping: requirements: type: seq description: List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to `follow_up_training`. - examples: + _examples: - | type: internal topic_name: statistics @@ -378,7 +378,7 @@ mapping: type: str description: | A copyright attribution string, as required by some licenses. - examples: + _examples: - © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors license: type: str @@ -393,7 +393,7 @@ mapping: description: | A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter) pattern: /^\/.*/ - examples: + _examples: - /assets/images/gat.png recordings: diff --git a/bin/schema-topic.yaml b/bin/schema-topic.yaml index 4297fa368765a6..f3d36b8a715565 100644 --- a/bin/schema-topic.yaml +++ b/bin/schema-topic.yaml @@ -7,7 +7,7 @@ mapping: pattern: /^[a-z0-9_-]+$/ description: | The internal identifier for a topic, it should be the same as the folder name. - examples: + _examples: - epigenetics - sequence-analysis - admin @@ -50,7 +50,7 @@ mapping: required: true description: | Title of the topic, this is displayed for users to see. - examples: + _examples: - Proteomics - Variant Analysis summary: @@ -58,13 +58,13 @@ mapping: required: true description: | A longer description of the contents of this topic - examples: + _examples: - Statistical Analyses for omics data and machine learning using Galaxy tools docker_image: type: str description: | The image ID for an image which contains all of the tools and data for this topic. - examples: + _examples: - quay.io/galaxy/sequence-analysis-training subtopics: type: seq @@ -80,14 +80,14 @@ mapping: pattern: /^[A-Za-z0-9_-]+$/ description: | Subtopic ID, this should match what is used in tutorials. - examples: + _examples: - single-cell title: type: str required: true description: | Subtopic title, which is displayed for users to see. - examples: + _examples: - Maintaining a Production Galaxy - Single-cell RNA-seq description: @@ -95,7 +95,7 @@ mapping: required: true description: | A human readable textual description of a subtopic. - examples: | + _examples: | - "Start here if you are new to RNA-Seq analysis in Galaxy" - "These tutorials take you from raw sequencing reads to pathway analysis" - "Tutorials about analysis of single-cell RNA-seq data" @@ -121,12 +121,12 @@ mapping: pattern: /^topic_[0-9]+$/ description: | An edam ontology id that describes the resource - examples: + _examples: - topic_3173 requirements: type: seq description: List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to `follow_up_training`. - examples: + _examples: - | type: internal topic_name: statistics @@ -156,7 +156,7 @@ mapping: references: type: seq - examples: | + _examples: | - | authors: "Vaudel M, et al." title: "Shedding light on black boxes in protein identification." @@ -181,7 +181,7 @@ mapping: type: str description: | Link to a gitter channel that is more relevant for this topic than the default. E.g. a single cell topic, you could use `Galaxy-Training-Network/galaxy-single-cell` to link to their specific chat room in all of the child tutorials by default. - examples: + _examples: - Galaxy-Training-Network/galaxy-single-cell - galaxy-genome-annotation/Lobby draft: @@ -200,7 +200,7 @@ mapping: description: | A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter) pattern: /^\/.*/ - examples: + _examples: - /assets/images/gat.png custom_css: type: str @@ -208,7 +208,7 @@ mapping: Any custom CSS you might want to apply to a specific topic. This could be overriding e.g. the masthead colour (beware, will potentially conflict with themes.) This is generally not a recommended property to set on topics, and something that is only used as part of outreach efforts to import content into the GTN. - examples: | + _examples: | - :root { --brand-color: red; } logo: @@ -225,6 +225,6 @@ mapping: The specific learning path you wish to reference as a call-to-action for views who aren't sure where to get started. It must be the name of a file in learning-pathways, without the `.md` suffix. This is not validated so, please make sure it's correct :) - examples: + _examples: - intro-to-galaxy-and-genomics - admin-training diff --git a/bin/schema-tutorial.yaml b/bin/schema-tutorial.yaml index 1cc6ca4c99ac4e..36e21513171d12 100644 --- a/bin/schema-tutorial.yaml +++ b/bin/schema-tutorial.yaml @@ -13,7 +13,7 @@ mapping: required: true description: | Title of the tutorial (it will appear on the tutorial page and the topic page) - examples: + _examples: - Clustering in Machine Learning - Breve introducción a Galaxy - en español - Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools @@ -24,7 +24,7 @@ mapping: required: true description: | list of questions that will be addressed in the tutorial - examples: + _examples: - How does Genome assembly work? - How do I change Galaxy configs? - How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset? @@ -42,7 +42,7 @@ mapping: - Compute (Skill) - multiple whole genome assemblies (Objective) - in such a way to develop big data processing skills (Result) - examples: + _examples: - Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis* - Explore Biodiversity data with taxonomic, temporal and geographical informations - Generate a DotPlot emulating the original paper using a different analysis tool @@ -56,7 +56,7 @@ mapping: of the tutorial. These should really be a key point, something that should stick in their mind; what you want them to take home from the tutorial. - examples: + _examples: - Pangeo ecosystem enables big data analysis in geosciences - "The MiModD suite of tools bundles most of the functionality required to perform mapping-by-sequencing analyses with Galaxy" - It can drastically simplify management of large numbers of VMs @@ -67,13 +67,13 @@ mapping: pattern: /^topic_[0-9]+$/ description: | An edam ontology id that describes the resource - examples: + _examples: - topic_3173 gitter: type: str description: | Link to a gitter channel that is more relevant for the tutorial than the default. E.g. a single cell tutorial could use `Galaxy-Training-Network/galaxy-single-cell` to link to their specific chat room. - examples: + _examples: - Galaxy-Training-Network/galaxy-single-cell - galaxy-genome-annotation/Lobby contributors: @@ -87,14 +87,14 @@ mapping: - ORGANISATIONS description: | List of tutorial contributors. Please use `contributions` instead as it provides more detailed accounting of tutorial history. - examples: + _examples: - hexylena - shiltemann contributions: required: true description: | List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial. - examples: | + _examples: | contributions: authorship: - shiltemann @@ -174,18 +174,18 @@ mapping: type: str description: | if the topic has [multiple subtopics defined](/training-material/topics/contributing/tutorials/create-new-topic/tutorial.html#adapt-the-metadata-for-your-topic), you can assign your tutorial to one of those subtopics here. Without this, the tutorial will appear in the "Other tutorials" section on the topic page. - examples: + _examples: - single-cell priority: type: int description: | This field allows ordering tutorials within the tutorial list. Tutorials with lower numbered priority come before tutorials with higher numbers. - examples: 1 + _examples: 1 zenodo_link: type: str description: | link on Zenodo to the input data for the tutorial - examples: + _examples: - "https://zenodo.org/record/3706539" pattern: /(^$|^https://zenodo.org/records?/[0-9]+/?$|^https://doi.org/10.5281/zenodo.[0-9]+/?$)/ extra: @@ -201,7 +201,7 @@ mapping: required: true description: | A free form list of tags that are relevant for your tutorial. - examples: + _examples: - covid-19 - git-gat translations: @@ -211,7 +211,7 @@ mapping: required: true description: | If alternative translations of a material are available, then use this key to indicate which languages have been manually translated. - examples: + _examples: - en abbreviations: type: map @@ -222,7 +222,7 @@ mapping: The expansion of the abbreviated term. description: | A dictionary of abbreviations and their expansions. - examples: | + _examples: | abbreviations: SQL: Structured Query Language API: Application Programming Interface @@ -244,7 +244,7 @@ mapping: pattern: /^(?:([0-9]*)[Hh])*(?:([0-9]*)[Mm])*(?:([0-9.]*)[Ss])*$/ description: | An estimation of the time needed to complete the hands-on. - examples: + _examples: - 10M - 1H30M redirect_from: @@ -253,11 +253,11 @@ mapping: - type: str description: | If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible. - examples: + _examples: - /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial notebook: type: map - examples: | + _examples: | notebook: language: python pyolite: true @@ -272,7 +272,7 @@ mapping: If you have an alternative preamble for your notebook that students should know before following (e.g. they must load X datasets in their history), it can be listed here. This text will be shown in the GTN tutorial, but it will **not** be included in the notebook, giving you a bit better control over mixing setup content which is relevant for Galaxy, with notebook content that can be easy to run for students. - examples: + _examples: - topics/climate/tutorials/pangeo-notebook/preamble.md pyolite: type: bool @@ -303,7 +303,7 @@ mapping: description: | A list of packages that must be installed before running this tutorial. This value is not currently used, but might be in the future. required: false - examples: + _examples: - tidyverse sequence: - type: str @@ -330,7 +330,7 @@ mapping: neural: type: bool required: true - examples: | + _examples: | voice: id: Lupe lang: es-US @@ -338,7 +338,7 @@ mapping: follow_up_training: type: seq description: list of resources that the reader of the material could follow at the end of the tutorial - examples: + _examples: - | type: internal topic_name: statistics @@ -385,7 +385,7 @@ mapping: requirements: type: seq description: List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to `follow_up_training`. - examples: + _examples: - | type: internal topic_name: statistics @@ -433,13 +433,13 @@ mapping: type: str description: | A copyright attribution string, as required by some licenses. - examples: + _examples: - © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors license: type: str description: | An [SPDX](https://spdx.org/) identifier for the alternative license that is used for that particular material. This is **only** relevant for materials which have been imported from an external source and were originally licensed under another license. For new materials we strongly encourage contributors to not use this key as materials are CC-BY, by default. - examples: + _examples: - MIT - Apache-2.0 draft: @@ -451,7 +451,7 @@ mapping: description: | A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter) pattern: /^\/.*/ - examples: + _examples: - /assets/images/gat.png hands_on: type: str @@ -463,11 +463,11 @@ mapping: type: str description: | link to the external tutorial - examples: + _examples: - "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#" answer_histories: type: seq - examples: | + _examples: | - label: "UseGalaxy.eu" history: https://humancellatlas.usegalaxy.eu/u/j.jakiela/h/generating-a-single-cell-matrix-using-alevin-3 - label: "Older Alevin version" @@ -486,7 +486,7 @@ mapping: pattern: /[0-9]{4,}-[0-9]{2}-[0-9]{2}/ input_histories: type: seq - examples: | + _examples: | input_histories: - label: "UseGalaxy.eu" history: https://humancellatlas.usegalaxy.eu/u/wendi.bacon.training/h/cs1pre-processing-with-alevin---input-1 diff --git a/faqs/galaxy/datasets_change_datatype.md b/faqs/galaxy/datasets_change_datatype.md index 32fe8f7a33abd0..3ac94d9d275172 100644 --- a/faqs/galaxy/datasets_change_datatype.md +++ b/faqs/galaxy/datasets_change_datatype.md @@ -5,6 +5,11 @@ area: datasets box_type: tip layout: faq contributors: [bebatut,nsoranzo,hexylena,shiltemann,ajadi-abiola,lldelisle,nekrut] +optional_parameters: + datatype: A string representing the Galaxy datatype +examples: + Assign datatype without specifying the datatype: {} + Assign datatype with a specific datatype: {datatype: 'fastqsanger'} --- * Click on the {% icon galaxy-pencil %} **pencil icon** for the dataset to edit its attributes diff --git a/faqs/galaxy/datasets_convert_datatype.md b/faqs/galaxy/datasets_convert_datatype.md index 7bd42c7c47ee4f..7469c366cdbd1e 100644 --- a/faqs/galaxy/datasets_convert_datatype.md +++ b/faqs/galaxy/datasets_convert_datatype.md @@ -5,6 +5,11 @@ area: datasets box_type: tip layout: faq contributors: [shiltemann,hexylena,lldelisle] +optional_parameters: + conversion: The datatype to convert the dataset to +examples: + Convert to BAM: + conversion: BAM --- * Click on the {% icon galaxy-pencil %} **pencil icon** for the dataset to edit its attributes diff --git a/faqs/galaxy/datasets_create_new_file.md b/faqs/galaxy/datasets_create_new_file.md index ed9c99ad1f7cd4..623bf47c25a7ed 100644 --- a/faqs/galaxy/datasets_create_new_file.md +++ b/faqs/galaxy/datasets_create_new_file.md @@ -5,6 +5,17 @@ area: datasets box_type: tip layout: faq contributors: [bebatut,shiltemann,wm75,hexylena,simonbray] +optional_parameters: + name: The name of the dataset + format: The format of the dataset + genome: The genome of the dataset + convertspaces: Ask the user to convert spaces to tabs in the settings +examples: + Creating a new file: {} + Creating a specific file: + name: "SARS-CoV-2 feature mapping" + format: "tabular" + convertspaces: "true" --- * Click {% icon galaxy-upload %} **Upload Data** at the top of the tool panel diff --git a/faqs/galaxy/datasets_import_via_link.md b/faqs/galaxy/datasets_import_via_link.md index 72bf730574c92a..e2399c0a976ff3 100644 --- a/faqs/galaxy/datasets_import_via_link.md +++ b/faqs/galaxy/datasets_import_via_link.md @@ -4,6 +4,33 @@ area: data upload box_type: tip layout: faq contributors: [bebatut,hexylena,mtekman,lecorguille,shiltemann,nomadscientist,nekrut,mblue9] +optional_parameters: + reset_form: Tell the user to reset the form first + collection: Adds step to click the collection button + collection_type: Suggests a collection type + link: (Deprecated) Instead of collections use a link-type input + link2: (Deprecated) Second link + format: Suggests a format for the user to set + genome: Suggests a genome for the user to set + pairswaptext: Provides a filter for the pair detection + collection_name_convention: Suggests a naming convention for the collection +examples: + Import a list of files: + collection: 'true' + collection_type: List + collection_name: raw_files + format: thermo.raw + Create a paired collection with a given naming scheme: + collection: 'true' + collection_type: Paired + collection_name_convention: "'<name>_<plate>_<batch>' to preserve the sample names, sequencing plate number and batch number." + collection_name: "Here we will write 'C57_P1_B1'" + genome: "GRCm38/mm10" + pairswaptext: "'SRR5683689_1' and 'SRR5683689_2'" + "Import an interval file with specified genome, though providing the links in a code block is preferred": + link: "https://zenodo.org/record/3254917/files/chr21.gtf" + format: interval + genome: mm9 --- * Copy the link location diff --git a/faqs/galaxy/datasets_rename.md b/faqs/galaxy/datasets_rename.md index f0e91a60ba0385..f81cf201c7d9bd 100644 --- a/faqs/galaxy/datasets_rename.md +++ b/faqs/galaxy/datasets_rename.md @@ -4,6 +4,12 @@ area: datasets box_type: tip layout: faq contributors: [bebatut,nsoranzo,shiltemann,wm75,hexylena] +optional_parameters: + name: The new name for the dataset +examples: + Without prescribing a name: {} + Suggest the user rename the dataset genomes.fa: + name: genomes.fa --- - Click on the {% icon galaxy-pencil %} **pencil icon** for the dataset to edit its attributes diff --git a/faqs/galaxy/interactive_tools_open.md b/faqs/galaxy/interactive_tools_open.md index 010d6bc4895663..2d1ee25df0beb3 100644 --- a/faqs/galaxy/interactive_tools_open.md +++ b/faqs/galaxy/interactive_tools_open.md @@ -4,6 +4,12 @@ area: interactive tools box_type: tip layout: faq contributors: [mgramm1] +required_parameters: + tool: The name of the interactive tool +optional_parameters: {} +examples: + Basic example: + tool: "Interactive tool" --- 1. Go to User > Active InteractiveTools diff --git a/faqs/galaxy/workflows_run_ds.md b/faqs/galaxy/workflows_run_ds.md index f52404d96f8607..2dc675f04c97f3 100644 --- a/faqs/galaxy/workflows_run_ds.md +++ b/faqs/galaxy/workflows_run_ds.md @@ -4,6 +4,11 @@ area: workflows box_type: hands_on layout: faq contributors: [hexylena] +optional_parameters: + dockstore_id: The Dockstore ID of the workflow you want to import + title: The title of the workflow you want to import, can be any text +examples: + Load a workflow by Dockstore ID: {dockstore_id: "github.com/jmchilton/galaxy-workflow-dockstore-example-1/mycoolworkflow", title: "My Cool Workflow"} --- {% if include.dockstore_id %} diff --git a/faqs/galaxy/workflows_run_trs.md b/faqs/galaxy/workflows_run_trs.md index 011330db2aacf1..b26f624049f9f6 100644 --- a/faqs/galaxy/workflows_run_trs.md +++ b/faqs/galaxy/workflows_run_trs.md @@ -4,6 +4,14 @@ area: workflows box_type: hands_on layout: faq contributors: [hexylena] +optional_parameters: + path: Path to the on-disk location of the .ga file + title: A descriptive title for the workflow, does not need to match the workflow file itself +examples: + Incredibly generic box that does not tell you which workflow to import: {} + Importing a QC workflow: {path: "topics/assembly/tutorials/largegenome/workflows/Galaxy-Workflow-Data_QC.ga", title:"Galaxy Workflow Data QC" } + Importing a pre-treatments workflow: {path: "topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga", title:"Pretreatments"} + --- {% if include.path %} diff --git a/faqs/gtn/fair_training.md b/faqs/gtn/fair_training.md index 6bd0ab3386de99..6072d520866a3e 100644 --- a/faqs/gtn/fair_training.md +++ b/faqs/gtn/fair_training.md @@ -8,6 +8,9 @@ contributors: [hexylena] This infrastructure has been developed in accordance with the FAIR (Findable, Accessible, Interoperable, Reusable) principles for training materials {% cite Garcia2020 %}. Following these principles enables trainers and trainees to find, reuse, adapt, and improve the available tutorials. +The GTN receives a 100% score on the [FAIR Checker](https://fair-checker.france-bioinformatique.fr/check), as noted in our recent [news post]({{ site.baseurl }}/news/2024/05/13/fair.html) + + 10 Simple Rules | Implementation in GTN framework --------------- | ------------------------------- Plan to share your training materials online | Online [training material portfolio](https://training.galaxyproject.org/), managed via [a public GitHub repository](https://github.com/galaxyproject/training-material) diff --git a/topics/admin/faqs/git-commit.md b/topics/admin/faqs/git-commit.md index 8c630bf5477af2..a1a3aa2d6c1dea 100644 --- a/topics/admin/faqs/git-commit.md +++ b/topics/admin/faqs/git-commit.md @@ -4,6 +4,11 @@ area: gat box_type: hands_on layout: faq contributors: [hexylena] +required_parameters: + page: The parent page object since we reference the page's title in the commit message +examples: + Using this snippet: + page: page --- It's time to commit your work! Check the status with diff --git a/topics/admin/faqs/missed-something.md b/topics/admin/faqs/missed-something.md index bcce8e92b992d1..7f0e8f22503e39 100644 --- a/topics/admin/faqs/missed-something.md +++ b/topics/admin/faqs/missed-something.md @@ -4,6 +4,11 @@ area: utilities box_type: comment layout: faq contributors: [hexylena] +required_parameters: + step: The GIT-GAT step number +examples: + Link to step 2: + step: '2' --- {% assign prevStep = include.step | plus: -1 %} diff --git a/topics/computational-chemistry/tutorials/zauberkugel/tutorial.md b/topics/computational-chemistry/tutorials/zauberkugel/tutorial.md index c756f918a12142..057438ce05297c 100644 --- a/topics/computational-chemistry/tutorials/zauberkugel/tutorial.md +++ b/topics/computational-chemistry/tutorials/zauberkugel/tutorial.md @@ -76,7 +76,7 @@ Firstly, we will retrieve the concatenated ePharmaLib subset representing *P. fa > > 1. Upload the dataset from the [Zenodo](https://zenodo.org) link provided to your Galaxy history. > -> {% snippet faqs/galaxy/datasets_import_via_link.md link="hhttps://zenodo.org/record/6055897/files/ePharmaLib_PHARAO_plasmodium.phar" %} +> {% snippet faqs/galaxy/datasets_import_via_link.md link="https://zenodo.org/record/6055897/files/ePharmaLib_PHARAO_plasmodium.phar" %} > > > ePharmaLib versions > >