Add SearchGUI support for InstaNovo and InstaNovo+

[BioGeek]

InstaNovo is a de novo peptide sequencing tool.

This PR adds SearchGUI support for InstaNovo v1.2.2 in three modes:

• InstaNovo: de novo peptide sequencing with the transformer-based InstaNovo model.
• InstaNovo+: de novo peptide sequencing with the diffusion-based InstaNovo+ model.
• InstaNovo with refinement: InstaNovo predictions refined with InstaNovo+.

Changes

• Adds GUI entries for:

  • InstaNovo
  • InstaNovo+
  • InstaNovo with refinement

• Adds GUI descriptions and documentation links for the new algorithms.

• Adds advanced settings for:

  • InstaNovo transformer model
  • InstaNovo+ diffusion model
  • number of beams
  • standard vs knapsack beam search
  • save all beam predictions
  • batch size
  • optional config path
  • force CPU execution

• Adds SearchCLI flags:

  • -instanovo
  • -instanovo_plus
  • -instanovo_refine
  • -instanovo_folder

• Allows de novo-only InstaNovo runs without a FASTA database.

• Keeps FASTA validation for database search engine runs.

• Adds progress parsing for InstaNovo prediction output.

• Handles non-zero InstaNovo process exits as failed runs.

• Improves cancellation handling for external InstaNovo processes.

• Adds documentation for local InstaNovo setup with uv.

De Novo End-To-End With PeptideShaker

Follow-up changes so a de novo only run flows all the way through to PeptideShaker:

• Requires a database only when a database search engine is selected; de novo only runs (including with PeptideShaker post-processing enabled) no longer demand a FASTA.
• Omits the -fasta_file argument when launching PeptideShaker for a de novo only run.
• Uses the .mzML extension for ThermoRawFileParser output, matching what the tool actually writes, so converted spectra are found on case-sensitive file systems (de novo engines read the spectrum file directly).
• Reports a clear error and cancels the run when an external tool cannot be started (e.g. ThermoRawFileParser when mono is missing) instead of failing later with a null process NPE.

Implementation Notes

• SearchGUI runs InstaNovo from a local InstaNovo checkout.
• The installation folder should be the InstaNovo repository root.
• SearchGUI resolves the executable from .venv/bin/instanovo, then instanovo in the selected folder, then instanovo from PATH.
• The three output types are kept separate:
  • .instanovo.csv
  • .instanovoplus.csv
  • .instanovo.refined.csv

Screenshots

Tests

Ran:

mvn -Dtest=eu.isas.searchgui.processbuilders.InstaNovoProcessBuilderTest,eu.isas.searchgui.cmd.SearchCLIInstaNovoTest,eu.isas.searchgui.gui.SearchGUIInstaNovoModelsTest test
mvn -DskipTests -Dmaven.javadoc.skip=true package

Merge Order

Recommended order:

1. Add InstaNovo and InstaNovo+ import support compomics-utilities#73
2. This PR
3. Add PeptideShaker import UI support for InstaNovo result files peptide-shaker#570
4. Add DeNovoGUI compatibility APIs to Utilities compomics-utilities#74
5. Add InstaNovo support to DeNovoGUI denovogui#53
6. Update SearchGUI recipe to 4.3.17 bioconda/bioconda-recipes#66604
7. Update PeptideShaker recipe to 3.0.13 bioconda/bioconda-recipes#66603
8. Expose InstaNovo workflows in online input form barsnes-group/peptide-shaker-online#30
9. Bump PeptideShaker wrappers for InstaNovo support galaxyproteomics/tools-galaxyp#828