Updating tools/cnvkit from version 0.9.10 to 0.9.11

[gxydevbot]

Hello! This is an automated update of the following tool: tools/cnvkit. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

I have updated tools/cnvkit from version 0.9.10 to 0.9.11.

Project home page: https://github.com/etal/cnvkit/releases

For any comments, queries or criticism about the bot, not related to the tool being updated in this PR, please create an issue here.

[bgruening]

@khaled196 do you want to have a look here?

[khaled196]

Hi @bgruening

I found the problem but how can I fix it? shall. I create a pull request for the original directory

The issue concerns the difference between the new version output data and the repo test data.

It can be solved by replacing

<output name="out_reference_cnn" file="reference.cnn" />

to 

<output name="out_reference_cnn" file="reference.cnn" ftype="tabular" compare="sim_size">
    <assert_contents><has_size value="3000" delta="2000" /></assert_contents>
</output>

In test 1 and test 2

[bgruening]

You can create a completely new PR or PR to the bots repo as you like. A new PR is easier and totally fine.

[bgruening]

Missed the PR this is very nice. Thanks @khaled196!

Are you already using the https://github.com/galaxyproject/galaxy-language-server ?

[khaled196]

@bgruening

This is the first to know about it. I used GitPod. However. this looks more specific to the galaxy.

Thanks for sharing this. I will be using this for future work

[bgruening]

Thanks for sharing this. I will be using this for future work

Cool, it will make your life easier for sure :)