Add toml datatype

[jj-umn]

Add toml datatype. MetaMorpheus proteomics application uses toml format for parameter configuration.

What did you do?

• Added the "toml" format to datatypes_conf.xml.sample

Why did you make this change?

The GalaxyP group plans to add Galaxy tools for the MetaMorpheus proteomics application from UW Madison.
https://github.com/smith-chem-wisc/MetaMorpheus
MetaMorpheus proteomics application uses toml format for parameter configuration.
I think it is sufficient to have this as just a subclass of Text.
I put with "Proteomics" datatypes, however, toml is a configuration format that could be used in other contexts.

How to test the changes?

(select the most appropriate option; if the latter, provide steps for testing below)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. toml should be an option when uploading a dataset.

License

• I agree to license these contributions under Galaxy's current license.
• I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the MIT license. If this condition is an issue, uncheck and just let us know why with an e-mail to galaxy-committers@lists.galaxyproject.org.

For UI Components

• I've included a screenshot of the changes

[bernt-matthias]

Hi @jj-umn.. Are you planning to wrap metamorpheus?

I also looked into this because a colleague was interested.

How do you plan to use toml files? In my preliminary thoughts about a wrapper I imagined to realize the toml inputs as config files.

[jj-umn]

@bernt-matthias I've started on MetaMorpheus. I know the PeptideShaker developers are also interested in including MetaMorpheus. As soon as I get the basics working, I'll create a pull request that we can work from.

[bernt-matthias]

@jj-umn this is great. I'm just wondering if a toml data type is needed. Do you plan to use this as input / output of the tool? What would be the advantage of this?

[jj-umn]

@bernt-matthias The calibration task outputs toml files (one for each mzml) that should be used in the GPTMD and Search tasks. In addition, I was planning to allow a user to input a toml file for configuration. I still thinking about whether to make a single metamorpheus.xml tool that could perform multiple "Tasks", or if it is better to have separate task tools: metamorpheus_calibration.xml, metamorpheus_g_ptm_d.xml, metamorpheus_search.xml. I currently putting just about everything in a macros.xml so that it could be done either way. Let me know if you have any thoughts about that. You can email me at jj@umn.edu

[bernt-matthias]

I think multiple tools might be more intuitive for users. If you go for a single tool than this might look pretty awkward in workflows, since all steps would have the same id (not sure if this can be changed in the workflow editor). If you got something then put open a PR on galaxyp and I'm happy to comment / review.