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Brings FBMN support for SIRIUS lcms processing #869

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Brings FBMN support for SIRIUS lcms processing #869

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632774b
Update reformat_quantification.py for FBMN SIRIUS
lfnothias Jan 30, 2024
bebf481
Add SIRIUS formatter
lfnothias Jan 30, 2024
3b528c1
Update input.xml for FBMN SIRIUS
lfnothias Jan 30, 2024
652acef
Update write_description.py for FBMN SIRIUS
lfnothias Jan 30, 2024
77a1b3a
Update test_tasks.csv for SIRIUS FBMN
lfnothias Jan 30, 2024
88485fa
Create placeholder for SIRIUS folder
lfnothias Jan 30, 2024
9b316f6
test MGF file
lfnothias Jan 30, 2024
8e95f30
Adding FBMN SIRIUS test feature table
lfnothias Jan 30, 2024
f13eb80
Remove placeholder
lfnothias Jan 30, 2024
11494a7
Rename SIRIUS.mgf to sirius_ms2_spectra.mgf
lfnothias Jan 30, 2024
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3 changes: 2 additions & 1 deletion feature-based-molecular-networking/feature-based-molecular-networking/input.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -165,13 +165,14 @@
<options>
<option value="MZMINE" 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="AGILENT" label="Agilent"/>
<option value="MZTABM" label="MzTab-M"/>
<option value="SIRIUS" label="SIRIUS"/>
</options>
<validator type="set"/>
<default value="MZMINE"/>
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3 changes: 2 additions & 1 deletion feature-based-molecular-networking/test-integration-workflow/test_tasks.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -20,4 +20,5 @@ d0b5249f7d69443a8adcb9e43ebcc0a2,fbmn IIN,view_all_clusters_withID
d513e6923920413a89f1669b16117e1d,fbmn with mzML files,file_summary
f932ba2238c04499b48c696008c33672,fbmn with IIN collapse,
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
1,075 changes: 1,075 additions & 0 deletions ...ecular-networking/test/reference_input_file_for_formatter/SIRIUS/sirius_feature_table.csv
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