Roary: adjust the command line to prevent intermediate file deletion?

[jennaj]

tool_id: toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy2

How the problem presents: Tool can fail when many inputs are given -- or not fail and just produce emtpy outputs, in particular the core alignment.

Possible solution (guess!): Add in -z to the command string? https://github.com/sanger-pathogens/Roary/issues/519

Alternative solutions might include: Have the tool just warn about GFFs left out of the final result, instead of failing? Output a better log? When the tool produces empty outputs users are confused about why, and if not "red" failure no bug report options, so may be a more common issue than we know about.

References:

• Several user issues at the developer's repo. https://github.com/sanger-pathogens/Roary/issues. Search with "proteome" or "core alignment".
• Questions at the Ghelp forum, example: https://help.galaxyproject.org/t/roary-troubleshooting-version-3-13-0-galaxy2-or-later/. More found by searching with keyword "roary" -- some were about the prior file naming issue but even once adjusted (by user or via the updated wrapper) -- the mystery about why empty results remains.
• Older tracking ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/293#issuecomment-1255461595

Xref: moved from https://github.com/galaxyproject/tools-iuc/issues/5205