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@@ -21,3 +21,4 @@ custom_css: static/custom.css | |
| sections: | ||
| - section_1.yml | ||
| - section_2.yml | ||
| - section_3.yml | ||
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| @@ -1,91 +1,99 @@ | ||
| id: section_1 | ||
| title: Example section | ||
| title: Creating sections | ||
| tabs: | ||
| - id: tools | ||
| title: Tools | ||
| heading_md: Common tools are listed here, or search for more in the full tool panel to the left. | ||
| - id: faqs | ||
| title: FAQs | ||
| heading_md: | | ||
| This is a section. A section is composed of a title (*"Creating sections"*) | ||
| and one or more tabs. Each tab is composed of a title (*"FAQs"*), heading | ||
| text (*this*) and a collection of collapsable items. | ||
| Sections are rendered from data specified in a YAML file. | ||
| The structure of the YAML file is important, and must follow the | ||
| [defined schema](/schema). The two sections below give examples of how | ||
| content can be nested in sections. | ||
| content: | ||
| - title_md: Can I write content in HTML? | ||
| description_md: | | ||
| Yes - any file/field that accepts markdown can also accept HTML, | ||
| for example: | ||
| # Accordion item schema: | ||
| # title_md: <str> # inline MD accepted e.g. *italics*, **bold**, `code` | ||
| # description_md: <str> | ||
| # inputs: <optional> | ||
| # - datatypes: # tool input 1 - two accepted datatypes | ||
| # - <str> | ||
| # - <str> | ||
| # label: <str optional> | ||
| # - datatypes: # tool input 2 - one accepted datatype | ||
| # - <str> | ||
| # label: <str optional> | ||
| # button_link: <str optional> | ||
| # button_md: <str optional> | ||
| # button_tip: <str optional> | ||
| # view_link: <str optional> | ||
| # view_md: <str optional> | ||
| # view_tip: <str optional> | ||
| - `intro.md` | ||
| - `heading_md` (in section.yml) | ||
| - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1" | ||
| 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=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" | ||
| title_md: FastQC - sequence quality reports | ||
| description_md: > | ||
| Before using your sequencing data, it's important to ensure that | ||
| the data quality is sufficient for your analysis. | ||
| inputs: | ||
| - label: Sequencing data for analysis | ||
| datatypes: | ||
| - fasta | ||
| - fastq | ||
| - bam | ||
| - sam | ||
| However, be careful about nesting HTML within markdown. Anything inside | ||
| an HTML element must also be HTML. The following would be invalid: | ||
| - id: workflows | ||
| title: Workflows | ||
| heading_md: > | ||
| A workflow is a series of Galaxy tools that have been linked together | ||
| to perform a specific analysis. You can use and customize the example workflows | ||
| below. | ||
| <a href="https://galaxyproject.org/learn/advanced-workflow">Learn more</a>. | ||
| content: | ||
| - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222" | ||
| button_tip: Import to Galaxy AU | ||
| title_md: Data QC | ||
| view_link: https://workflowhub.eu/workflows/222 | ||
| view_tip: View in WorkflowHub | ||
| view_icon: tutorial | ||
| <pre class="prettyprint"> | ||
| <p> | ||
| This is a paragraph with a | ||
| [broken link](https://example.com). | ||
| </p> | ||
| </pre> | ||
| - title_md: Can I use variables in my content? | ||
| description_md: | | ||
| Report statistics from sequencing reads. | ||
| <br><br> | ||
| Tools: | ||
| Yes! Using variables is a great way to make a Lab page reuable across | ||
| Galaxy servers. | ||
| Variables defined in the base.yml/server.yml file can be used anywhere | ||
| that markdown or HTML content is provided. This includes templates like | ||
| `intro.md` and also section.yml `*_md` values. Any arbitrary variable | ||
| that you set in the base.yml/server.yml file can be used in the content: | ||
| 1. `base.yml` or `[server].yml`: | ||
| <pre class="prettyprint lang-yaml"> | ||
| myvar: foo | ||
| </pre> | ||
| 2. `intro.md`: | ||
| <pre class="code"> | ||
| # Analysis methods | ||
| This is a great place for doing analysis such as {{ myvar }}. | ||
| </pre> | ||
| - `nanoplot` | ||
| - `fastqc` | ||
| - `multiqc` | ||
| - button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=223" | ||
| button_tip: Import to Galaxy AU | ||
| 3. `section_1.yml`: | ||
| <pre class="prettyprint lang-yaml"> | ||
| ... | ||
| – title_md: Can I use variables in my YAML and Markdown/HTML content? | ||
| description_md: | | ||
| Yes, you can use variables like {{ myvar }}. | ||
| </pre> | ||
| - title_md: Can I exclude an item from specific hosts? | ||
| description_md: | | ||
| Estimates genome size and heterozygosity based on counts of kmers. | ||
| <br><br> | ||
| Tools: | ||
| Yes, you can exclude any component in the section schema from specific | ||
| hosts by listing hostnames under the | ||
| [exclude_from directive](/schema#tabitem). | ||
| This can be used to exclude items describing server-specific features, | ||
| such as: | ||
| - `meryl` | ||
| - `genomescope` | ||
| title_md: Kmer counting to estimate genome size | ||
| view_link: https://workflowhub.eu/workflows/223 | ||
| view_tip: View in WorkflowHub | ||
| <pre class="prettyprint lang-yaml"> | ||
| - 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. | ||
| exclude_from: | ||
| - usegalaxy.org | ||
| </pre> | ||
| - id: help | ||
| title: Help | ||
| content: | ||
| - button_md: More info | ||
| button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/ | ||
| - title_md: Can I add images into Markdown/HTML? | ||
| description_md: | | ||
| You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy. | ||
| Just look for the "Upload data" button at the top of the tool panel. | ||
| title_md: How can I import my genomics data? | ||
| - description_md: | | ||
| We recommend subsampling large data sets to test tools and workflows. | ||
| A useful tool is `seqtk_seq`, setting the parameter at "Sample fraction of sequences". | ||
| title_md: How can I subsample my data? | ||
| Yes, you can use standard Markdown or HTML syntax to include images. | ||
| When adding the `src` atrribute to an image tag, you can use relative | ||
| URLs to specify an image located in your content directory, or an | ||
| absolute URL to an image hosted elsewhere on the web: | ||
| Using Markdown: | ||
| <pre class="code"> | ||
|  | ||
| </pre> | ||
| Using HTML (allows custom styling): | ||
| <pre class="code"> | ||
| <img src="./static/images/myimage.png" alt="My Image" width="200" height="200"> | ||
| </pre> | ||
| With a full URL: | ||
| <pre class="code"> | ||
| [](https://example.com/myimage.png) | ||
| </pre> |
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