Move CIGAR creation to GAFA?

[nsoranzo]

@anilthanki Since the only tool that needs the alignments in CIGAR format is GAFA, what about moving the t_coffee_to_cigar.py script from t_coffee to the GAFA tool and make it accept alignments in fasta_aln format? That would save the creation of the CIGAR output collection (thousand of datasets).

Obviously after PAG XXV.

[nsoranzo]

This would also reduce our modifications to the t_coffee Galaxy wrapper. I was not able to find any reference for the use of CIGAR for multiple sequence alignment on Google, so I think that option can be safely removed.