diff --git a/workflows/proteomics/openms-metaprosip/.dockstore.yml b/workflows/proteomics/openms-metaprosip/.dockstore.yml new file mode 100644 index 000000000..a6407d1d1 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/.dockstore.yml @@ -0,0 +1,10 @@ +version: 1.2 +workflows: +- name: main + primaryDescriptorPath: /metaprosip.ga + subclass: Galaxy + testParameterFiles: + - /metaprosip-tests.yml + authors: + - name: Matthias Bernt + orcid: 0000-0003-3763-0797 diff --git a/workflows/proteomics/openms-metaprosip/.workflowhub.yml b/workflows/proteomics/openms-metaprosip/.workflowhub.yml new file mode 100644 index 000000000..28b3e2b22 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: metaprosip/main diff --git a/workflows/proteomics/openms-metaprosip/CHANGELOG.md b/workflows/proteomics/openms-metaprosip/CHANGELOG.md new file mode 100644 index 000000000..a023e8e99 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2023-04-13 +First release. diff --git a/workflows/proteomics/openms-metaprosip/README.md b/workflows/proteomics/openms-metaprosip/README.md new file mode 100644 index 000000000..d0bb6c82c --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/README.md @@ -0,0 +1,26 @@ +# 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 diff --git a/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml new file mode 100644 index 000000000..d3be8fe73 --- /dev/null +++ b/workflows/proteomics/openms-metaprosip/metaprosip-tests.yml @@ -0,0 +1,39 @@ +- 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 + - 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