Merge pull request #172 from bernt-matthias/topic/metaprosip

Add MetaproSIP

workflows/proteomics/openms-metaprosip/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  primaryDescriptorPath: /metaprosip.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /metaprosip-tests.yml
+  authors:
+  - name: Matthias Bernt
+    orcid: 0000-0003-3763-0797

workflows/proteomics/openms-metaprosip/.workflowhub.yml

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+version: '0.1'
+registries:
+- url: https://workflowhub.eu
+  project: iwc
+  workflow: metaprosip/main

workflows/proteomics/openms-metaprosip/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2023-04-13
+First release.

workflows/proteomics/openms-metaprosip/README.md

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+# MetaProSIP: automated inference of elemental fluxes in microbial communities
+
+## Inputs dataset
+
+- `Centroided LC-MS datasets` in mzML (MetaProSIP is mainly tested on data generated by orbitrap instruments)
+- `Fasta Database` in Fasta (aminoacid sequences)
+
+## Inputs values
+
+- `Precursor monoisotopic mass tolerance` (ppm): This value is passed to
+  - MSGFPlusAdapter parameter `Precursor monoisotopic mass tolerance` (-precursor_mass_tolerance)
+  - MetaProSIP parameter `Tolerance in ppm` (-mz_tolerance_ppm)
+- Fixed modifications
+- Variable modifications
+- Labeled element
+
+## Processing
+
+- DecoyDatabase: Add decoy sequences to the Fasta database (for FDR calculation)
+- FeatureFinderCentroided: identify eluting peptides that correspond to isotopologues with natural isotopic distributions 
+- MSGFPlusAdapter: identify peptides through peptide fragment fingerprinting (database search)
+- FeatureFinderMultiplex: detect elution profiles of unlabeled peptides
+- PeptideIndexer: annotate protein association to identified peptides
+- FalseDiscoveryRate: Calculate FDR
+- IDMapper: map identified spectra to elution profiles
+- MetaProSIP: calculate the protein-SIP features, to perform functional grouping, and for protein inference

workflows/proteomics/openms-metaprosip/metaprosip-tests.yml

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+- doc: Test outline for MetaProSIP
+  job:
+    Fasta Database:
+      class: File
+      location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_1and2_454AllContigs_HEX.fasta
+      filetype: fasta
+    Centroided LC-MS datasets:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Zeitz_SIP_13-II_020_picked.mzML
+        location: https://abibuilder.cs.uni-tuebingen.de/archive/openms/galaxy-testdata/metaprosip/Zeitz_SIP_13-II_020_picked.mzML
+        filetype: mzml
+    Precursor monoisotopic mass tolerance (ppm): 10.0
+    Fixed modifications: Carbamidomethyl (C)
+    Variable modifications: Oxidation (M)
+    Labeled element: C
+  outputs:
+    Peptide centric result:
+      element_tests:
+        Zeitz_SIP_13-II_020_picked.mzML:
+          asserts:
+          - that: has_n_lines
+            n: 85
+          - that: has_text
+            text: Peptide Sequence
+          - that: has_text
+            text: AATGTPSPAGSPPPIVPAPK
+    Feature fitting result:
+      element_tests:
+        Zeitz_SIP_13-II_020_picked.mzML:
+          asserts:
+          - that: has_n_lines
+            n: 4091
+          - that: has_text
+            text: Group 1
+          - that: has_text
+            text: LYSFHTLHQTYMK