Question: Format code (XML, bash) in a Galaxy page
gravatar for timothee.flutre
4.2 years ago by
timothee.flutre0 wrote:

I am writing a page describing to other users of my Galaxy instance how to add a new tool. Here is what I did:

  1. log in to my Galaxy instance
  2. click on "User"
  3. click on "Saved Pages"
  4. click on "Add new page"
  5. fill the form and click on "Submit"
  6. the new page opens itself in the "editing mode"

It is in such a page that I would like to add a few lines of XML as well as bash as examples. For the moment, for bash, I'm using "Paragraph type" > "Block quote". It's not perfect, but it works. However, for XML, even with this, it seems to be interpreted by Galaxy when I click on "View" (after saving and closing the editing interface). As a result, the XML I wrote disappears as soon as I save and close the page.

On GitHub, when adding an issue, one can use the markdown syntax (details here). Does such a thing exist for Galaxy? In the Galaxy editing interface, there is a "Paragraph type" menu with, among others, "Preformatetd" and "Blockquote". But these options don't seem to correspond to the visual display of code. Or am I missing something?

(I edited my question on 10/3, I hope it is clearer now.)

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ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by timothee.flutre0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool in the Tool Shed includes plain text XML in the help section. It should be a good example to follow:

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k

Thanks, but when I click on the link I end up here and the sections I see are "Repository revision", "Repository 'toolfactory'", "Repository README files", etc, but no "Help".

ADD REPLYlink written 4.2 years ago by timothee.flutre0

Just scroll to the bottom on the page to view what the help text looks like. Then clone the repository and examine the xml wrapper for the tool. You can also look at the top level wrapper files by logging into the Tool Shed and choosing "view repository tip files" from the menu.

Hope this helps, Jen, Galaxy team

ADD REPLYlink written 4.2 years ago by Jennifer Hillman Jackson25k

Sorry, I think my initial question wasn't clear. I edited it substantially, I hope it is clearer now.

ADD REPLYlink written 4.2 years ago by timothee.flutre0
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