Add cooler zoomify

[tbrown91]

Hello,

We would like to include the zoomify function from cooler to be able to view these in higlass. I have made an initial effort on this front, but maybe you would prefer to change it to your specs.

All the best,

Tom

[tbrown91]

thanks Björn, I think this is what I'm after.

I'm just a little nervous as I can't get planemo running on my laptop and don't see the checks running

[bgruening]

You are a new contributor and github prevents CI runs for them, security ...

Feel free to let me know why planemo is not running for you via chat.

[tbrown91]

I am getting the following linting error, which I don't understand when compared to other xmls in this suite:

.. ERROR: Invalid XML found in file: cooler_zoomify.xml. Errors [/var/folders/gf/k37ckmns0lx_fryk50s01j9h0000gq/T/tmp2428wkkl:33:0:ERROR:SCHEMASV:SCHEMAV_CVC_COMPLEX_TYPE_3_2_1: Element 'data', attribute 'type': The attribute 'type' is not allowed.]

[tbrown91]

... I found it

[tbrown91]

I think this is good to go now. I passed the planemo tests and don't think I did anything too controversial

[bgruening]

Thanks @tbrown91!

[lldelisle]

Hi,
I've just launched the CI. Tell me it passes.

[lldelisle]

Hi,
It seems you added to the repo a input.mcool which is not used. Is it normal? It seems that you use the 'input.cool' that I put.

[tbrown91]

ah, you're right. I think I created this in one of my initial tests. I will remove it

[lldelisle]

In the current test, it is not adding any resolution, here is the standard error:

INFO:cooler.cli.zoomify:Recursively aggregating "/tmp/tmpvf9z3tb7/files/5/6/b/dataset_56b365ac-4545-40dc-9db7-38908595e4b3.dat"
INFO:cooler.cli.zoomify:Writing to "/tmp/tmpvf9z3tb7/job_working_directory/000/2/outputs/dataset_376f04ff-763d-4065-bcd9-aa1fb9f49ec8.dat"
INFO:cooler.reduce:Copying base matrices and producing 1 new zoom levels.
INFO:cooler.reduce:Bin size: 1000000

Can you add another test with for example resolution 1000000,2000000,10000000?

[lldelisle]

I forgot to tell you that I am super happy that you are contributing (I am really rude, I should have started by this).

[tbrown91]

no worries.

See what you think

[lldelisle]

Perfect. Thank you.