Add converter for Kraken to BIOM.

[davebx]

Concerns: For the tests to work, the JSON output is prettified. This results in somewhat larger output files.

[davebx]

Ping @jxtx due to expressed interest.

[bgruening]

@davebx I feel not confident to review the converter but the wrappers looks great! So :+1 from me.

[blankenberg]

Suggest:

• add shebang to top of .py files.
• add __version__ string constant and --version argument
• Move the converter code to a separate package repository, where installing it will chmod +x the .py using the xml tags. Should also be able to require eg a python package. Now, script can be called by name directly, without specifying interpreter
• Add options to allow overriding column selections, so that any 'tabular' file can be used as input (tabular to biom converter), defaults can be set to kraken columns. can also hide under advance options (your choice)

[blankenberg]

That being said, i am +1 on merging this, if additional time is not available for changes.

[bgruening]

@davebx your call! Thanks Dan!

[bgruening]

ping @davebx

[blankenberg]

made a pr against @davebx https://github.com/davebx/tools-iuc/pull/4

[blankenberg]

One important issue is that we should be using the taxonomy found in the kraken database directories, not the separately maintained ncbi taxonomy.

[davebx]

I wasn't sure this should be applied to the master branch. Then I remembered that this is tools-iuc, not galaxy.

[nsoranzo]

@davebx Can you fix the 6 flake8 errors in https://travis-ci.org/galaxyproject/tools-iuc/jobs/147195352#L443 ?

[shiltemann]

@davebx oof, this one is ancient, still relevant you think? We might be able to use this kraken-biom bioconda package to perform this task?

[bernt-matthias]

Closing this in favor of https://github.com/galaxyproject/tools-iuc/pull/4763