Add DIA-NN (#719)

* Initial commit * Add test * Add test-data * Fix lint error * Fix lint error * Fix command not found * Change --threads count to Galaxy env variable * Change .name to .element_identifier * Change .name to .element_identifier * single-quotes * Change .name to .element_identifier * Fix string * Remove test for bruker files --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyproteomics · Jun 26, 2023 · 21426ab · 21426ab
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diff --git a/tools/diann/.shed.yml b/tools/diann/.shed.yml
@@ -0,0 +1,13 @@
+categories:
+  - Proteomics
+description: DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.
+long_description: |
+  DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing. It can be used for both library-based and library-free analysis, and it supports all types of DIA/SWATH acquisitions.
+homepage_url: https://github.com/vdemichev/DiaNN
+name: diann
+owner: galaxyp
+remote_repository_url: https://github.com/vdemichev/DiaNN
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for {{ tool_name }}"
diff --git a/tools/diann/diann.xml b/tools/diann/diann.xml
diff --git a/tools/diann/test-data/ThyroglobMRM000003.d.tar b/tools/diann/test-data/ThyroglobMRM000003.d.tar
diff --git a/tools/diann/test-data/bruker-report-lib.tsv b/tools/diann/test-data/bruker-report-lib.tsv
@@ -0,0 +1 @@
+FileName	PrecursorMz	ProductMz	Tr_recalibrated	IonMobility	transition_name	LibraryIntensity	transition_group_id	decoy	PeptideSequence	Proteotypic	QValue	PGQValue	Ms1ProfileCorr	ProteinGroup	ProteinName	Genes	FullUniModPeptideName	ModifiedPeptide	PrecursorCharge	PeptideGroupLabel	UniprotID	NTerm	CTerm	FragmentType	FragmentCharge	FragmentSeriesNumber	FragmentLossType	ExcludeFromAssay
diff --git a/tools/diann/test-data/bruker-report.tsv b/tools/diann/test-data/bruker-report.tsv
@@ -0,0 +1 @@
+File.Name	Run	Protein.Group	Protein.Ids	Protein.Names	Genes	PG.Quantity	PG.Normalised	PG.MaxLFQ	Genes.Quantity	Genes.Normalised	Genes.MaxLFQ	Genes.MaxLFQ.Unique	Modified.Sequence	Stripped.Sequence	Precursor.Id	Precursor.Charge	Q.Value	PEP	Global.Q.Value	Protein.Q.Value	PG.Q.Value	Global.PG.Q.Value	GG.Q.Value	Translated.Q.Value	Proteotypic	Precursor.Quantity	Precursor.Normalised	Precursor.Translated	Translated.Quality	Ms1.Translated	Quantity.Quality	RT	RT.Start	RT.Stop	iRT	Predicted.RT	Predicted.iRT	First.Protein.Description	Lib.Q.Value	Lib.PG.Q.Value	Ms1.Profile.Corr	Ms1.Area	Evidence	Spectrum.Similarity	Averagine	Mass.Evidence	CScore	Decoy.Evidence	Decoy.CScore	Fragment.Quant.Raw	Fragment.Quant.Corrected	Fragment.Correlations	MS2.Scan	IM	iIM	Predicted.IM	Predicted.iIM
diff --git a/tools/diann/test-data/bsa.fasta b/tools/diann/test-data/bsa.fasta
@@ -0,0 +1,12 @@
+>bsa sp|P02769|ALBU_BOVIN Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4
+MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPF
+DEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEP
+ERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYY
+ANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVA
+RLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKE
+CCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRR
+HPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK
+LGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL
+NRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLP
+DTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVV
+STQTALA
diff --git a/tools/diann/test-data/report-lib.tsv b/tools/diann/test-data/report-lib.tsv
@@ -0,0 +1 @@
+FileName	PrecursorMz	ProductMz	Tr_recalibrated	IonMobility	transition_name	LibraryIntensity	transition_group_id	decoy	PeptideSequence	Proteotypic	QValue	PGQValue	Ms1ProfileCorr	ProteinGroup	ProteinName	Genes	FullUniModPeptideName	ModifiedPeptide	PrecursorCharge	PeptideGroupLabel	UniprotID	NTerm	CTerm	FragmentType	FragmentCharge	FragmentSeriesNumber	FragmentLossType	ExcludeFromAssay
diff --git a/tools/diann/test-data/report.tsv b/tools/diann/test-data/report.tsv
@@ -0,0 +1 @@
+File.Name	Run	Protein.Group	Protein.Ids	Protein.Names	Genes	PG.Quantity	PG.Normalised	PG.MaxLFQ	Genes.Quantity	Genes.Normalised	Genes.MaxLFQ	Genes.MaxLFQ.Unique	Modified.Sequence	Stripped.Sequence	Precursor.Id	Precursor.Charge	Q.Value	PEP	Global.Q.Value	Protein.Q.Value	PG.Q.Value	Global.PG.Q.Value	GG.Q.Value	Translated.Q.Value	Proteotypic	Precursor.Quantity	Precursor.Normalised	Precursor.Translated	Translated.Quality	Ms1.Translated	Quantity.Quality	RT	RT.Start	RT.Stop	iRT	Predicted.RT	Predicted.iRT	First.Protein.Description	Lib.Q.Value	Lib.PG.Q.Value	Ms1.Profile.Corr	Ms1.Area	Evidence	Spectrum.Similarity	Averagine	Mass.Evidence	CScore	Decoy.Evidence	Decoy.CScore	Fragment.Quant.Raw	Fragment.Quant.Corrected	Fragment.Correlations	MS2.Scan	IM	iIM	Predicted.IM	Predicted.iIM
diff --git a/tools/diann/test-data/small-peakpicking-cwt-allMS.mzML b/tools/diann/test-data/small-peakpicking-cwt-allMS.mzML