dada2 fixes

[bernt-matthias]

detected here #2701

• data manager: real bug fix
• bug fix in makeSequencTable: cheetah for testing plot variable was wrong
• allow larger delta for tests on Rdata and pdf (mostly 1/2 file size, but anyway less then the file size .. essentially now a test for file presence)

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
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[bgruening]

@bernt-matthias can you maybe use galaxyproject/galaxy#8852 ... and just check for size. This way we also remove the Rdata from the repo.

[bernt-matthias]

Not sure if file size is the same on all systems since the files can be compressed with different methods or even uncompressed.

We could fix to uncompressed. Which would be faster, but require a bit more space. My guess would be that the file size might be the same on all systems.

[bgruening]

You have a delta in there as well: https://github.com/galaxyproject/galaxy/pull/8852/files#diff-4191170733b24a9e99ba70b64c8b8787R30

[mvdbeek]

Oh yeah, it's not in master yet, I'll do that. There's also galaxyproject/galaxy#9054 to look out for.

[mvdbeek]

master is updated now

[bernt-matthias]

@bgruening sounds good. just was wondering if --update_test_data updates the numbers ..? Probably not... :)

[bernt-matthias]

Seems that also galaxyproject/galaxy#8852 has not found its way to master and 19.09 which would be necessary. .. and I think also the xsd of planemo.

[bernt-matthias]

Anyway, I just updated the test and do not see the advantage here: We can't remove the test outputs, since subsequent steps of the dada2 pipeline use them as input.

My last commit could be easily undone if you agree.

[bgruening]

Imho it makes a lot of sense for PDF ... that tools read Rdata is not good, security wise. But I guess this is unrelaed to this PR.

[bernt-matthias]

that tools read Rdata is not good, security wise. But I guess this is unrelaed to this PR.

still did not get this point. as far as I see it nothing is executed on import.

[bernt-matthias]

@mvdbeek to make this work we need galaxyproject/galaxy#8852 in master and 19.09 .. and I think also the xsd of planemo needs an update

[mvdbeek]

It isn't a bug, I don't think we can do a backport. But it might not be required if we start using using the proper galaxy packages instead of galaxy-lib in planemo. @nsoranzo was working on this.
Can we just work with the delta for now ?

[bernt-matthias]

yep. will reset to 770ea38