Again a 1000 apologies for the late night errors. I focused on the explanations, and not on the script which I cobbled together for the post without testing. The original didn't have the test try: except: else:

The corrected script with the error is: https://pastebin.com/PYXb52Xa#QErrPuTP

@Eliria, I have focused only on the keyboard, I rarely use the mouse. To highlight text for a script, I navigate with the keyboard keys. A primeval habit picked up before the dinosaurs' extinction, and never tried the middle button with the clipboard.

#SECONDARY is officially not-recommended, but probably used. Some offline apps interfere with copy and paste, and sometimes the results include text of the previous copy and paste.

Yeah, I'm also a keyboard user, but am non-conventional (my favorite ways of getting and pasting text are Shift+Delete and Shift+Insert and some programs (and even Kubuntu) don't recognize those by default, causing some wrestling over here. I also never used the middle mouse button, but was curious about it for this particular use. Thanks for your description of offline apps interfering with copying and pasting. That explains the odd behavior I'm seeing.

The above comment was really for Elliria. I should have made that explicit.

If the goal is to wrap the selected text with ref tags, I've got 15 selection wrapper scripts in AutoKey. Here's one of them that I just now tested on a 100-character block of text and it works for me:

# This script replaces the selected string with a new string wrapped in the specified wrapper tags.
# Select some text in any window and click this script in the AutoKey context menu or press its hotkey.

# If a selection was made:
try:
    target = clipboard.get_selection()
    keyboard.send_keys("<ref>%s</ref>" % target)
# If no selection was made:
except:
    # Let the user know no selection was made:
    dialog.info_dialog(title="Error", message="No text was selected.")

Although it's true that #SECONDARY is mostly extinct, it still exists and is still mentioned in web pages online, so it's worthy of noting, especially since we can access it from within AutoKey. It's testing it that's tricky, because it's tough to tell if we have software capable of it.

Here's another of my 15 selection-wrapper scripts that toggles the wrapper, adding it if it's not there or removing it if it is:

# This script replaces the selected string with a new string with the specified wrapper tags added if not present or removed if present.
# Select some text in any window and click this script in the AutoKey context menu or press its hotkey.

# If a selection was made:
try:
    # Store the selected text in a local variable:
    target = clipboard.get_selection()

    # Pause for a moment:
    time.sleep(0.2)

    # Check if the selected text contains wrapper tags:
    if "<ref>" not in target: 
        # Add wrapper tags if it doesn't:
        keyboard.send_keys("<ref>%s</ref>" % target)

    # Otherwise, if it has wrapper tags:
    else:
        # Delete the wrapper tags:
        keyboard.send_keys(target.replace("<ref>","").replace("</ref>",""))

# If no selection was made:      
except:
    # Let the user know no selection was made:
    dialog.info_dialog(title="Error", message="No text was selected.") 

Last, but not least, here's yet another of my 15 selection-wrapper scripts that doesn't replace the selected text, but leaves it undisturbed while it wraps itself around it:

# This scripts wraps text around the selection without manipulating the selection in any way.
# The script gets the contents of the clipboard (the selection) only to count its length.
# It then moves the cursor to the beginning of the selection in the focused window.
# It then inserts the specified opening wrapper text.
# It then moves the cursor to the end of the selection in the focused window.
# It then inserts the specified closing wrapper text.

# If a selection was made:
try:
    # Get the selection:
    text = clipboard.get_selection()
    # Get the length of the selection:
    length = len(text)
    # Move the cursor to the beginning of the selection:
    keyboard.send_keys("<left>")
    # Insert opening wrapper text:
    keyboard.send_keys("<ref>")
    # Move the cursor to the end of the selection:
    keyboard.send_key("<right>", repeat=length)
    # Insert closing wrapper text:
    keyboard.send_keys("</ref>")
# If no selection was made:
except:
    # Let the user know no selection was made:
    dialog.info_dialog(title="Error", message="No text was selected.")

@josephj11, @Elliria, I found the webpage mentioned earlier. It's the clearest step by step explanation of the X-clipboard. Please help by adding it where you think it should be placed. X selections ...

Actually it was hiding in plain sight on the first line of our clipboard article. I added a couple of notes at the end of the existing article with another link to it and a few other tidbits.

Thanks. That page also links to a page on the Wayback Machine that might be of interest.

That page is interesting, but is written for application programmers and doesn't seem to add anything that an AutoKey user would need to know. I just skimmed it, so I may have missed something good...

I figured @ineuw might find something useful in it.

Oh, gosh, @josephj11, I should have seen that coming.

Aw, here's a [virtual hug] for you, @ineuw. I hope your load lightens up soon.

@ineuw Sometimes tool building seems to take more time than using them saves!

Tool building has been my favorite programming thing since I learned how to code. I'm always looking for ways to optimize my work flow and customize things to work "my way" - which is quite often different from what anybody else wants.

I pay for this highly when I have to do a fresh install of Linux. It usually takes me a couple of weeks to get everything back the way I want it.

I'm still trying to come up with better way to remember all my changes. I get the most obvious ones and discover the rest when I try to do things and they don't work as expected.

Thanks for the help. I am not too sure if I want the load to lighten. :-) It's a wonderful challenge re-learn what I forgot. I will revisit the help page, and add the link to the article that gave me the clearest explanation of the X clipboard and helped me to properly word this post.

I use Zim for that, @josephj11 (it's in the Ubuntu repositories), with a page dedicated to the comprehensive steps for making all my usual changes to a fresh installation of GNU/Linux and then updating that as needed. I'd be lost without a personal wiki.

Yep, although you can use its interface as well, in which case it works like a word processor. My reason for choosing it was that MoinMoin didn't keep up with Python 3 [sigh] and I had to switch to something and this was, first of all, the only personal wiki I could find that didn't require running a server and truly is personal and, second of all, stores everything in plain text, so it's searchable with locate, grep, KRunner, and any other search programs. I've got an ever-growing AutoKey page in mine as well and won't be surprised to find that you will, too.

I currently have a whole directory under $HOME/Public/howto/Autokey with 45 files in it. I don't think I'll import them all. I also have a hundred or more other files in folders at the same level as the Autokey folder. Importing all of that would take some work.