assignment.md

Assignment:

Use the code in this repository to create a Galaxy tool, that will convert a given single Galaxy dataset from the .mgf format to the .mat format.

The result of this assignment should at minimum include an .xml file with the Galaxy tool definition. You can also include a paragraph or two explaining your thinking about the asignment or describe the steps taken. We will take these notes into consideration when evaluating.

You do not have to include parameters other than what is needed for the conversion. We will evaluate by putting your tool in Galaxy and running it on the test data provided in the /test-data directory. The result is most probably correct if the following Galaxy Tool test passes:

    <tests>
        <test>
            <param name="input_file" value="test.mgf"/>
            <output name="output_file" file="test.mat"/>
        </test>
    </tests>

Hints and links:

• Your best friend for Galaxy tool development is a utility called planemo. See the docs.
• Moreover Planemo documentation contains section on writing Galaxy tools.
• The most important planemo commands for you are planemo serve and planemo test. Full list of commands.
• Don't miss the README.md file in this repository.
• Galaxy itself implements the mgf format, but not the mat format. Set the output format to generic txt to work around this.
• You do not need to care about cornercases or invalid inputs.
• You can check out the full XML schema of what is allowed in a Galaxy tool file.
• If you are stuck please feel free to write an email to [email protected] and ask specific questions. This is encouraged and not penalized.