Bug: Cutadapt 3.5+galaxy1 parameter --strip-suffix

[jennaj]

Message for end-users:

1. How to notice if you hit the bug?

• The "submit" button for CutAdapt redirects to the top of the tool form. Does not actually submit.
• No confirmation messages in the center panel, no new dataset(s) in the history.

2. How to workaround the bug?

• Click on "Read Modification Options" to expand the section.
• Scroll down to the "Strip suffix" section (will be highlighted by a light blue box).
• Type one or more characters (any!) into that parameter, then remove those characters until empty again.
• Scroll down and click on the "submit" button again.
• The tool will now execute!

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Developers:

The option --strip-suffix is for some reason flagged as required upon job submission (blocks the submission, and shouldn't). But if the user "touches" that parameter's free text input (adds then removes any content, even a single character), the requirement is satisfied, and the job submits.

1. That shouldn't be needed
2. It isn't obvious what is going wrong because that section is collapsed at the default and the rerun tool form view (I had help from a person that submitted a bug report who noticed/described the exact problem!)
3. Only happens at usegalaxy.org -- could this be related to 22.01??
4. Another odd workaround -- load up the tool form from a prior version of this tool using "rerun", switch to the 3.5+galaxy1 version, adjust the inputs/settings (doesn't need to include this param) -- and submit works.
5. This tool is included in tutorials.
6. Introduced in this version of the tool added to org in Dec 2021 Update cutadapt on usegalaxy.org #447

Test histories:

• org (requires workaround - single or paired) https://usegalaxy.org/u/jen/h/test-cutadapt-35galaxy1
• eu (does not need any workaround) https://usegalaxy.eu/u/jenj/h/test-cutadapt-35galaxy1

Tests (those failures are due to a metadata issue, but the tests that never ran might be due to this)

• Test cutadapt 3.5+galaxy1 mvdbeek/usegalaxy-tests#22

ping @dannon @davebx @mvdbeek @natefoo

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Screenshots

Before submit

After submit AND expanding that section

Fiddle with the parameter, and the job submits

[mvdbeek]

This isn't needed anymore, the fix is deployed on usegalaxy.org

[jennaj]

Fixed in galaxyproject/galaxy#13523

Will be live at usegalaxy.org before Monday, March 24, 2022