Modify default outputs

[asetGem]

The content of the result directory will now contain, by default, only the tab file, with information on all integrons found, for all replicons of the input file.

Todo:

• [x] Check that there is a 'replicon' column in the final tab. If not, add it, to deal with multi-fasta input files
• [x] By default:
  • [x] Do not generate pdf file
  • [x] do not generate gbk file
  • [x] Remove temporary files (others folder)
• [x] Add an option --pdf to generate the pdf file when activated
• [x] Add an option --gbk to generate gbk file when activated. => When multi-fasta:
  • [x] 1 gbk/replicon
  • [ ] or 1 final multi-gbk at the end ??
• [x] Add an option --tmp to keep tmp files at the end of run
• [x] When input is in multi-fasta, concatenate the tab results of all replicons in one and generate this file at the end of run

[bneron]

commit 86a6f39 add support of option --pdf or --gbk to generate the pdf or genbank file