[FBMN] Adding support for SIRIUS processing. Updating Optimus and MetaboScape converters

feature-based-molecular-networking/Makefile

@@ -3,5 +3,5 @@ include ../Makefile.deploytemplate
 
 WORKFLOW_NAME=feature-based-molecular-networking
 TOOL_FOLDER_NAME=feature-based-molecular-networking
-WORKFLOW_VERSION=release_28.2
+WORKFLOW_VERSION=release_29
 WORKFLOW_DESCRIPTION='Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The supported tools are: MZmine, OpenMS, MS-DIAL, MetaboScape, XCMS, Progenesis QI, and the mzTab-M format. FBMN facilitates the detection of isomers that are separated by chromatographic or ion mobility separation, and provides accurate ion abundances for statistical analysis. Note that FBMN requires processing the mass spectrometry data with a feature detection and alignment tool. For rapid/qualitative analysis, we recommend using classical molecular networking that accepts unprocessed mass spectrometry files. See the FBMN documentation at https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking and refer to the "Method and Citation for Manuscripts" on the results page for citations.'

feature-based-molecular-networking/README.md

@@ -39,18 +39,48 @@ Additionally, it is assumed there are additional columns where the per sample qu
 
 The MGF output should contain the "SCANS" header, and it must correspond to the identifier of the "row ID". It has to be unique, and can be non sequential.
 
-### Metaboscape
+### MetaboScape
+
+#### For MetaboScape 5.0
 
 The feature quantification table (.CSV file, comma separated) should include columns with the following header:
 
-1. FEATURE_ID
-2. RT
-3. PEPMASS
-4. MaxIntensity
+1. SHARED_NAME
+2. FEATURE_ID
+3. RT
+4. PEPMASS
+5. CCS (optional, only tims/PASEF data)
+6. SIGMA_SCORE
+7. NAME_METABOSCAPE
+8. MOLECULAR_FORMULA
+9. ADDUCT
+10. KEGG
+11. CAS
+12. MaxIntensity
+13. {GroupName}_MeanIntensity (0-n times, dependent on the groups defined in MetaboScape)
+14. Sample Intensities
+
+All sample headers are not including the file format extension ".d" (DDA) or ".tdf" (PASEF). The columns "FEATURE_ID", "RT", "PEPMASS", "MaxIntensity" are mandatory. 
+Important: In the metadata table, the filename MUST NOT HAVE the extension suffixe indicated.
+
+#### Earlier versions of MetaboScape (<5.0)
 
-For ion mobility data, it must include a "CCS" column.
+The feature quantification table (.CSV file, comma separated) should include columns with the following header:
 
-All sample headers are not including the file format extension ".d" (DDA) or ".tdf" (PASEF) 
+1. SHARED_NAME
+2. FEATURE_ID
+3. RT
+4. PEPMASS
+5. NAME
+6. MOLECULAR_FORMULA
+7. ADDUCT
+8. KEGG
+9. CAS
+10. {GroupName}_MeanIntensity (0-n times, dependent on the groups defined in MetaboScape)
+11. Sample Intensities
+
+Sample headers are including the file format extension ".d". The columns "FEATURE_ID", "RT", "PEPMASS", "CAS" are mandatory. 
+Important: In the metadata table, the filename MUST HAVE the ".d" extensionsuffixe.
 
 ### Progenesis QI
 
@@ -91,3 +121,13 @@ The feature quantification table (.TXT format, tab-separated) should include a h
 Following these headers are the samples. 
 
 The MGF output should contain the "SCANS" header, and it must correspond to the identifier of the "row ID". It has to be unique, and can be non sequential.
+
+### SIRIUS
+
+The feature quantification table (.CSV file, comma separated) should have three columns named:
+
+1. row ID
+2. row m/z
+3. row retention time
+
+The native sample headers from SIRIUS don't include the "Peak area" suffix, so the converter add that suffix for internal processing.

feature-based-molecular-networking/feature-based-molecular-networking/input.xml

@@ -165,12 +165,13 @@
             <options>
                 <option value="MZMINE2" label="MZmine"/>
                 <option value="OPENMS" label="OpenMS"/>
-                <option value="OPTIMUS" label="Optimus"/>
+                <option value="OPTIMUS" label="Optimus (Legacy)"/>
                 <option value="MSDIAL" label="MS-DIAL"/>
                 <option value="METABOSCAPE" label="MetaboScape"/>
                 <option value="XCMS3" label="XCMS"/>
                 <option value="PROGENESIS" label="Progenesis QI"/>
                 <option value="MZTABM" label="MzTab-M"/>
+                <option value="SIRIUS" label="SIRIUS (Experimental)"/>
             </options>
             <validator type="set"/>
             <default value="MZMINE2"/>

feature-based-molecular-networking/test-integration-workflow/test_tasks.csv

@@ -19,5 +19,7 @@ d0b5249f7d69443a8adcb9e43ebcc0a2,fbmn IIN,view_all_clusters_withID
 8c6b9e069b5843229e0902fd55086022,fbmn with blank molecules pre-removed,
 d513e6923920413a89f1669b16117e1d,fbmn with mzML files,file_summary
 f932ba2238c04499b48c696008c33672,fbmn with IIN collapse,
+6aa41748ea3c4872aca7f5e86c7f69c4,fbmn mzmine2 with topk library search,
 9f2c15c889504df38d7730243b7b0619,fbmn mzmine2 with topk library search,
-debbc6b5e28445789005d465226661e5,fbmn with no library matches,
+debbc6b5e28445789005d465226661e5,fbmn with no library matches,
+333295a1b04c4267863a1f8f7cbf6364,fbmn SIRIUS,view_all_clusters_withID