Mothur: fixed issues with chimera tools

[oxyko]

Issue described in #419. Also, added test data and test for chimera.slayer. But test is commented out, because planemo wasn't able to run it. Will need to revisit it once mothur wrapper tests are in good shape.

[martenson]

Thanks for the contribution @oxyko
Is it possible to trim the testing dataset to be less than 25k lines? It would help preventing this repo from growing too big.

[oxyko]

Will do.

[bgruening]

@oxyko this file is still 17.000 lines, is this correct?
tools/mothur/tools/mothur/test-data/chimera_test_in.fasta

[bgruening]

Can you please rebase/squash against master to get rid of the large file from the git history? Thanks!

Let me know if you need help with squashing commits.

[martenson]

http://gitready.com/advanced/2009/02/10/squashing-commits-with-rebase.html

[oxyko]

I've removed the test files and tried the rebase/squash, but I'm afraid I'm in a bit of a mess and my HEAD is now detached. Could you see if you can bring in the current pull as it is? If not, I'll do the hard reset on mothur branch, redo the changes and do a new pull request.

[bgruening]

I guess we can merge this branch and ry to rebase the master mothur branch before merging into main. @martenson does this sound reasonable? If so please feel free to merge.

[oxyko]

Thanks guys! I'll try and be more careful with rebasing and test data size next time.

[martenson]

@bgruening I tried to do the rebase locally and it is not easy. If you see the diff in GitHub you will notice that only one or two commits are actually being shown - all other changes are both commited and then reverted resulting in every commit having conflicts while rebasing (e.g. all the whitespace changes are missing). This needs some handwork :/

[oxyko]

OK, doing a hard reset on mothur and re-applying the changes.

[bgruening]

@oxyko thanks. Just to explain the mess. We try to keep this repository as small as possible, hence we try to keep test data small.
@martenson thanks for investing!