User Guide Lacks Sufficient Details

[DarioS]

README.rst needs more information. For instance, a lot of databases are required (e.g. --TE, --rnadb, --estdb). Where can users download suitable databases for human cancer genomics analysis? What output files does the software produce and what are the columns representing? What are the files in test-data folder and what is the expected output if software was installed correctly?

[ppouchin]

Hi,

Are you using that software from the command line? This was primarily developed to be used from Galaxy, as mentioned in the paper.
The test-data folder is used by Planemo to run tests automatically, the expected results are included (res.html and res_files/).

I only fixed parts of the tool, and I'm not a biologist, so I don't want to say something wrong, but the databases you mention might be available from UCSC or NCBI.