Make guppyplex input handling more flexible

[wm75]

This allows the user to specify which sequence input files guppyplex
should collapse into a single output, and which ones it should keep
separate. Also makes the tool work with fastq and fastq.gz data alike
and exposes the --quality threshold parameter.

The changeset also contains a fix for the artic minion pipeline, which
should make it handle input data with spaces in its name.

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)

[wm75]

Currently I cannot fully test this locally because my conda fails to resolve the bioconda artic package's dependencies.
Curious to see whether that will work here.

[pvanheus]

Currently I cannot fully test this locally because my conda fails to resolve the bioconda artic package's dependencies. Curious to see whether that will work here.

The artic bioconda package is rather huge, and best installed with mamba. (We have actually switched to using Singularity in Galaxy to a large extent because of this package!)

[wm75]

Currently I cannot fully test this locally because my conda fails to resolve the bioconda artic package's dependencies. Curious to see whether that will work here.

The artic bioconda package is rather huge, and best installed with mamba. (We have actually switched to using Singularity in Galaxy to a large extent because of this package!)

I'm impressed: conda chewed on this for hours without success before I killed it. mamba resolved things in under 30 secs!
Thanks for the hint @pvanheus !