Add compress option pairtool wrapper

[Smeds]

This update adds support for compressed input and output in the pairtools wrapper. Since pairtools determines whether to use compression based on the file extension—which must be .gz—the wrapper has been updated to automatically create input and output links with the appropriate .gz suffix.

For output, compression can be enabled by setting the compress_output parameter to true, ensuring that the generated output link ends with .gz. For input, the wrapper depends on the file types being 4dn_pairs.gz or 4dn_pairsam.gz, which ensures that the input files also have the required .gz extension.

This pull-request have new data types that currently aren't in the galaxy repository, which will result in failed tool linting.

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)

[Smeds]

Pull-request #20634 will add the new formats used by this update.

[Smeds]

@nsoranzo I have updated the tool wrapper according to your comments. It will now rely more in the input format to decide if the output will be compressed, except for parse which generate the pairsam files. The linting is still failing and I guess it will do that until the format update is moved into the master branch.

[Smeds]

@nsoranzo when is galaxy-tool-util update. Looks like this library needs update for my pull-request to pass the linting.

[Smeds]

@nsoranzo @mvdbeek @jmchilton Would it be possible to get a new release of galaxy-tool-util with the updated pairtool datatype?

And if we need to wait for the next release. Could someone approve this pull-request even though the linting fails?