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Fix -H double role as file and list of groups

Workum, Dirk-Jan van requested to merge fix_homology_file_msa into pantools_v3.5

The issue that arose was the -H is used for both homology group files and homology group identifiers according to the code. However, the argument parsing assumed it always was a file. We should therefore split the argument based on what it means.

I let -H be used for homology group files and -G for a list of homology groups. Both are comma-separated still. I also created an ArgGroup class for them being mutually exclusive. NB: I introduced one unresolved issue: providing a string to -G gives a weird error message that I cannot handle with bean validation?

  • Fix weird error message with -G and a non-integer input.

IMPORTANT: This is a merge request to the pantools_v3.5 branch, which will later on be merged into master.

Edited by Workum, Dirk-Jan van

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