Cleanup repository (#239)

* Remove old conversion scripts (mostly implemented in psm_utils now) * Docs: Move webserver api docs from wiki to readthedocs; Update docs on spectrum file input * Remove old train script (outdated; to be moved to docs) * Update readme (add missing correlate-single)
compomics · Jan 20, 2025 · 366583c · 366583c
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diff --git a/README.rst b/README.rst
@@ -57,6 +57,7 @@ The MS³PIP Python application can perform the following tasks:
 - ``predict-batch``: Predict fragmentation spectra for a batch of peptides.
 - ``predict-library``: Predict a spectral library from protein FASTA file.
 - ``correlate``: Compare predicted and observed intensities and optionally compute correlations.
+- ``correlate-single``: Compare predicted and observed intensities for a single peptide spectrum.
 - ``get-training-data``: Extract feature vectors and target intensities from observed spectra for
   training.
 - ``annotate-spectra``: Annotate peaks in observed spectra.

diff --git a/conversion_tools/MSF_to_MS2PIP_SpecLib.py b/conversion_tools/MSF_to_MS2PIP_SpecLib.py