Merge branch 'develop' of https://github.com/OpenMS/OpenMS into more_doc

enetz · Feb 12, 2024 · 4f538f8 · 4f538f8
2 parents a48194d + 7ffeae5
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diff --git a/CHANGELOG b/CHANGELOG
@@ -18,8 +18,11 @@ PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
 
 What's new:
 - Breaking change: Rename of parameters for FeatureFinderCentroided (debug->advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
+
 Library:
 - Extend FileHandler to support load and store operations for our major datastructures (spectra, features, identifications, etc.). Replaced file type specific code with the more generic FileHandler calls to decouple the IO code from other parts of the library.
+- SiriusAdapter reworked to SiriusExport: Instead of running SIRIUS directly, this reworked tool takes multiple mzML and feautureXML (optional) files exporting a single SIRIUS .ms input file as well as an input table with compound info from features for the new AssayGeneratorMetaboSirius tool. (#7234)
+- Splitting AssayGeneratorMetabo into two tools: In line with the changes to SiriusExport this tool has been split into two separate workflows. AssayGeneratorMetabo generates an assay library from mzML and feautreXML files using an heuristic approach picking the highest intensity MS2 peaks (like before). AssayGeneratorMetaboSirius takes an existing SIRIUS project directory as input to generate an assay library based on fragmentation trees. (#7234)
 - better documentation for all SpectraFilter... tools (#7183)
 
 Fixes:
@@ -469,7 +472,7 @@ New tools:
   - OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
   - OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL)
   - PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL)
-  - SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
+  - SiriusExport -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
   - XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)
 
 Deprecated and removed tools:

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -249,15 +249,6 @@ if(CLANG_TIME_TRACE)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ftime-trace")
 endif()
 
-#------------------------------------------------------------------------------
-# Enable SIRIUS_test (SiriusAdapter/AssayGeneratorMetabo)
-#------------------------------------------------------------------------------
-option(ENABLE_SIRIUS_TEST "Enable test for SIRIUS (SiriusAdapter)" OFF)
-
-#------------------------------------------------------------------------------
-# Enable CSI:FingerID_test (SiriusAdapter)
-#------------------------------------------------------------------------------
-option(ENABLE_FINGERID_TEST "Enable test for CSI:FingerID (SiriusAdapter)" OFF)
 
 #------------------------------------------------------------------------------
 # Enable Coverage

diff --git a/cmake/knime_package_support.cmake b/cmake/knime_package_support.cmake
@@ -202,7 +202,6 @@ set(THIRDPARTY_ADAPTERS
     "CometAdapter"
     "PercolatorAdapter"
     "MSFraggerAdapter"
-    "SiriusAdapter"
     "NovorAdapter"
   )
 

diff --git a/doc/doxygen/public/TOPP.doxygen b/doc/doxygen/public/TOPP.doxygen
@@ -152,6 +152,7 @@
 
   <b>Targeted Experiments and OpenSWATH</b>
   - @subpage TOPP_AssayGeneratorMetabo - Generates an assay library using DDA data (Metabolomics).
+  - @subpage TOPP_AssayGeneratorMetaboSirius - Generates an assay library using SIRIUS project directory (Metabolomics).
   - @subpage TOPP_ClusterMassTracesByPrecursor - Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
   - @subpage TOPP_MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
   - @subpage TOPP_MRMPairFinder - Evaluates labeled pair ratios on MRM features.
@@ -192,7 +193,7 @@
   <b>Metabolite Identification</b>
   - @subpage TOPP_AccurateMassSearch - Finds potential HMDB IDs within the given mass error window.
   - @subpage TOPP_MetaboliteSpectralMatcher - Identifies small molecules from tandem MS spectra.
-  - @subpage TOPP_SiriusAdapter - De novo metabolite identification.
+  - @subpage TOPP_SiriusExport - Export for Sirius de novo metabolite identification.
 
   <b>RNA</b>
   - @subpage TOPP_NucleicAcidSearchEngine - Search MzML files for oligonucleotides and their modifications.

diff --git a/doc/doxygen/public/developer_tutorial.doxygen b/doc/doxygen/public/developer_tutorial.doxygen
@@ -210,7 +210,7 @@ The extensible %OpenMS library implements common mass spectrometric data process
         - Accurate mass search: 
             - Tool AccurateMassSearch
         - De novo identification:
-            - Tool SiriusAdapter
+            - Tool SiriusExport
 
 <br>
 - General:
@@ -273,7 +273,7 @@ Within the ANALYSIS folder, you can find several important tools
 <br>
 
 
-For the sake of completeness you will find a short list of the THIRDPARTY tools, which are integrated via wrappers into the %OpenMS framework (usually called -Adapter e.g. SiriusAdapter)
+For the sake of completeness you will find a short list of the THIRDPARTY tools, which are integrated via wrappers into the %OpenMS framework (usually called -Adapter e.g. CometAdapter)
 
 Wrapper to third-party tools:
     - Search Engines (MSGFPLUS, XTandem, Comet)

diff --git a/src/openms/include/OpenMS/ANALYSIS/ID/SiriusAdapterAlgorithm.h b/src/openms/include/OpenMS/ANALYSIS/ID/SiriusAdapterAlgorithm.h