Update Maker: Add parameter -fix_nucleotides

[gallardoalba]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

This PR includes the -fix_nucleotides parameter. This is required when input sequences contain non-IUPAC characters. It solves the error reported in https://help.galaxyproject.org/t/how-to-do-augustus-training-or-maker-training/6221/5?u=gallardoalba

[bgruening]

can you also use a macro here for the 1 with VERSION_SUFFIX https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-versions

[gallardoalba]

Sure, do you think this parameter should be enabled by default?

[bgruening]

If we have this by default, our bot can bump the version number automatically.