Fix -H double role as file and list of groups

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.

docs/source/msa.rst

@@ -30,7 +30,8 @@ created with **FastTree**.
   from the list above requires use of the ``--method`` argument. For
   aligning multiple homology groups, please use
   ``--method=multiple-groups`` with the homology groups specified in a
-  csv file on a single line (can be added with ``--homology-file=/path/to/hm.csv``.
+  csv file on a single line (can be added with
+  ``--homology-file=/path/to/hm.csv`` or ``--homology-groups=2,3,4,4``).
   For aligning regions, please use ``--method=regions`` with a regions
   file that is added with ``--regions-file=/path/to/rf.txt``. For aligning
   sequences based on a functional domain, please use
@@ -99,7 +100,10 @@ Options
      - Exclude a selection of genomes.
    * - ``--homology-file``/``-H``
      - A text file with homology group node identifiers, separated by a comma.
-       Default is all homology groups.
+       Default is all homology groups. (Mutually exclusive with ``--homology-groups``.)
+   * - ``--homology-groups``/``-G``
+     - A comma separated list of homology group node identifiers.
+       Default is all homology groups. (Mutually exclusive with ``--homology-file``.)
    * - ``--regions-file``/``-R``
      - A text file containing genome locations with on each line: a genome
        number, sequence number, begin and end position, separated by a space.