Add Wordcloud

[524D]

Added wcloud.

I still need to merge changes that were made in the meantime, but can you please check if things look okay?

[vedran-kasalica]

Hi @524D, thank you for making the PR the changes look good! I see that the tool.json file is missing cwl_implementation field (see documentation, specifically text above "Adding New Tools from bio.tools Not Present in cwl-tools").

The newest APE-2.4 version dev3 generates cwl_implementation field as well (it just has to be updated to point to GitHub).

Finally, it would also be nice at some point to include the Dockerfile under cwl-tools/wcloud/docker, similar was done for MSAmana. I shared with you access to the Workflomics account on DockerHub via LastPass, in case you want to upload the images under Workflomcis.

[524D]

Hi @vedran-kasalica, thanks for your remarks. I've updated the files and merged changes that were done in the meantime. According to GitHub it can now be merged, but I still have done insufficient testing, especially of the CWL. Is an easy way to do this?

I will include the Dockerfile at a later point, it's now in a separate repository.

Edit: I've tested with cwl-runner by creating a wordcloud from a license file. It works as expected, so I hope perform correctly in the workflomics benchmarks.

[kretep]

@524D If you want, you could add a test script similar to that in Sage-proteomics: https://github.com/Workflomics/tools-and-domains/tree/main/cwl-tools/Sage-proteomics/test

If you name the script "run-cwl.sh", it will be included in the automated tests. You'll need to put your data somewhere, or indeed just link to a random text file and have "input.yml" refer to that.

[vedran-kasalica]

Hi Rob, thank you for updating the PR, the tool looks ready to be used within Workflomics! Feel free to merge it into main.

Regarding your question about testing, Peter started implementing automated tests by adding sh scripts to tool dirs see Sage. Here, run_cwl.sh annotates the command to run the cwl using cwltool and the predefined inputs.yml. If you wish you can add a similar file to your repo to trigger the automated test, but this could be done in a separate PR.