diff --git a/tools/metfrag/.shed.yml b/tools/metfrag/.shed.yml new file mode 100644 index 00000000000..c0c90c5f8fe --- /dev/null +++ b/tools/metfrag/.shed.yml @@ -0,0 +1,7 @@ +categories: + - Metabolomics +description: MetFrag performs annotation of tandem mass spectra of metabolites. Candidate molecules of different databases are fragmented in silico and matched against mass MS/MS spectra. +homepage_url: http://c-ruttkies.github.io/MetFrag/ +name: metfrag +owner: iuc +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/metfrag/ diff --git a/tools/metfrag/metfrag-cli-batch.xml b/tools/metfrag/metfrag-cli-batch.xml new file mode 100644 index 00000000000..6dbcfe36ac8 --- /dev/null +++ b/tools/metfrag/metfrag-cli-batch.xml @@ -0,0 +1,149 @@ + + + + + Run MetFrag with a given parameter set. + + metfrag + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark + + | **Tool update: See the 'NEWS' section at the bottom of the page** + + --------------------------------------------------- + + .. class:: infomark + + **Authors** + + | **Payam Emami (payam.emami@medsci.uu.se)** and **Christoph Ruttkies (christoph.ruttkies@ipb-halle.de)** wrote and maintain this wrapper for MetFrag batch mode processing. + + --------------------------------------------------- + + .. class:: infomark + + **Please cite** + + Ruttkies, C., Schymanski, E. L., Wolf, S., Hollender, J. and Neumann, S. MetFrag relaunched: incorporating strategies beyond in silico fragmentation. J Cheminform 8:3, (2016) DOI: 10.1186/s13321-016-0115-9 + + --------------------------------------------------- + + ===================== + MetFrag CLI Batch + ===================== + + ----------- + Description + ----------- + + | This module is used to run MetFrag on annotated MS/MS spectra for compound annotation. The parameters are set by **msms2metfrag**. + + + ----------- + Input files + ----------- + + +------------------------------+------------+ + | File | Format | + +==============================+============+ + | 1) File with MetFrag | txt | + | parameters | | + +------------------------------+------------+ + | 2) Database File (optional) | csv | + +------------------------------+------------+ + + ---------- + Parameters + ---------- + + File with MetFrag parameters + | File containing MetFrag parameters which is generated by **msms2metfrag** + | + + Additional Parameters + | Additional parameters that can be passed to MetFrag. This can include e.g. access information for a local MetChem database instance + | + + Database File + | File containing candidates used as database + | + + Additional MetFrag scores + | Add additional MetFrag scores used to score candidates + | + + ------------ + Output files + ------------ + + metfrag_cli_batch_output_1.csv + | A csv output file with scored candidates and properties + | + + --------------------------------------------------- + + ---- + NEWS + ---- + + CHANGES IN VERSION 0.3 + ======================== + + - added support for additional MetFrag scores + + CHANGES IN VERSION 0.2 + ======================== + + - added support for a local file database + + + CHANGES IN VERSION 0.1 + ======================== + + First version + + + + 10.1186/s13321-016-0115-9 + + + + + + + diff --git a/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv new file mode 100644 index 00000000000..a2bbb5e03f2 --- /dev/null +++ b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.csv @@ -0,0 +1,72 @@ +Score,MonoisotopicMass,SMILES,InChIKey,NoExplPeaks,NumberPeaksUsed,InChI,MaximumTreeDepth,Identifier,ExplPeaks,InChIKey3,InChIKey2,InChIKey1,IUPACName,FragmenterScore,MolecularFormula,FragmenterScore_Values,FormulasOfExplPeaks,XlogP3 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b/tools/metfrag/test-data/1_746.022_716.5434_1569591.66000003_PE_PG_AutoMS_2-B_3_03_18583.mzML.txt @@ -0,0 +1,12 @@ +DatabaseSearchRelativeMassDeviation=10 +FragmentPeakMatchAbsoluteMassDeviation=0.01 +FragmentPeakMatchRelativeMassDeviation=10 +MetFragDatabaseType=LocalCSV +MetFragScoreTypes=FragmenterScore +NeutralPrecursorMass=715.534338937996 +IsPositiveIonMode=True +PrecursorIonType=[M+H]+ +MetFragPeakListReader=de.ipbhalle.metfraglib.peaklistreader.FilteredStringTandemMassPeakListReader +MetFragCandidateWriter=CSV 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