Move Galaxy tools to the eBCSgen repository

[mopichalova]

Moved the top-level API functions from the galaxytools repository to /api directory in this repository, the eBCSgen repository.
No modifications were made to the scripts or the original repository.

Close #115

[xtrojak]

We don't want to move Galaxy tools here - only the top-level API functions (.py files). All the XML files, test data, or shed file don't belong here. And also it does not belong to Galaxy subdirectory (this should be actually removed one day when all "local" issues are resolved - e.g. properly sharing visualisations).

[mopichalova]

We don't want to move Galaxy tools here - only the top-level API functions (.py files). All the XML files, test data, or shed file don't belong here. And also it does not belong to Galaxy subdirectory (this should be actually removed one day when all "local" issues are resolved - e.g. properly sharing visualisations).

Thank you for your feedback regarding the structure of the repository. I have made the necessary changes as per your suggestions. Moved the top-level API functions to directory in the root of this repository (commit 5eca9c2) and removed all xml files, test data and the Galaxy subdirectory, ensuring that only the relevant Python files remain (commit 5eca9c2).

[xtrojak]

This is a good start, but I would improve it in following ways:

1. Rename the api folder to eBCSgen/API - we want it to be inside the Python package to make it available for imports
2. Define the argument parsing using argparse inside if __name__ == '__main__': section to allow calling it from the command line, but define the top level function separately - a random example demonstrating this.
3. (optional) Create __init__.py file in the API folder alongside with all the top-level scripts, importing all top-level functions in one place. This can simplify importing the functions when using the eBCSgen library. Another random example.
4. Update readthedocs documentation - maybe there is some argparse integration, you have to check.