BedTools:MultiCovBed new version not working

I have been using MultiCovBed occasionally. Lately it simply doesn’t work regardless of the files loaded (ERROR: Unrecognized parameter: -f , although I used the default).
While several weeks ago the versions used were:
|Galaxy Tool Version:||
|Tool Version:|bedtools v2.27.0|

Now it states:
|Galaxy Tool Version:|2.27.1|
|Tool Version:|bedtools v2.16.1|

Seems like an updated version of Galaxy Tool (2.27.1 vs 2.27.0) uses a downgraded version of bedtools (2.27.0 vs 2.16.1)

How can I overcome this and run the tool without an error just as before?


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Hello, That seems odd. I’ll do some testing on the newer tool wrapper.

Meanwhile, try switching to using a prior version of the tool that worked for you. Do this by loading up the tool form and clicking on the “Versions” menu at the top. For this tool, the choices available are:

More feedback once review/testing complete.

Thanks for reporting the problem!

Thanks a lot for the prompt reply.
Yup, switching to the previous version (2.27.0) works perfect!
Thanks for the tip, never used it before (or: never had to use it before…).

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Update: We found the missing tool dependencies and are correcting. If interested, this is the ticket:

Once fixed/tested the ticket will close out and the newer version of all Bedtools tools can be used if you want. Some do have bug fixes.

Thanks again for reporting the problem!