.gitignore
.gitmodules
.pre-commit-config.yaml
AGENTS.md
CHANGELOG.md
CITATION.cff
COMMANDS.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
uv.lock
.github/workflows/ci.yml
.github/workflows/conda-build.yml
data/ontologies/bto.parquet
data/ontologies/chebi.parquet
data/ontologies/cl.parquet
data/ontologies/clo.parquet
data/ontologies/efo.parquet
data/ontologies/mondo.parquet
data/ontologies/ncbitaxon.parquet
data/ontologies/ncit.parquet
data/ontologies/pato.parquet
data/ontologies/pride.parquet
data/ontologies/psi-ms.parquet
data/ontologies/uberon.parquet
data/ontologies/unimod.parquet
recipe/meta.yaml
scripts/generate_cli_docs.py
src/sdrf_pipelines/__init__.py
src/sdrf_pipelines/_version.py
src/sdrf_pipelines/config.py
src/sdrf_pipelines/openms.tsv
src/sdrf_pipelines/parse_sdrf.py
src/sdrf_pipelines.egg-info/PKG-INFO
src/sdrf_pipelines.egg-info/SOURCES.txt
src/sdrf_pipelines.egg-info/dependency_links.txt
src/sdrf_pipelines.egg-info/entry_points.txt
src/sdrf_pipelines.egg-info/requires.txt
src/sdrf_pipelines.egg-info/top_level.txt
src/sdrf_pipelines/converters/__init__.py
src/sdrf_pipelines/converters/base.py
src/sdrf_pipelines/converters/maxquant/__init__.py
src/sdrf_pipelines/converters/maxquant/maxquant.py
src/sdrf_pipelines/converters/maxquant/modifications.xml
src/sdrf_pipelines/converters/maxquant/param2sdrf.yml
src/sdrf_pipelines/converters/msstats/__init__.py
src/sdrf_pipelines/converters/msstats/msstats.py
src/sdrf_pipelines/converters/normalyzerde/__init__.py
src/sdrf_pipelines/converters/normalyzerde/normalyzerde.py
src/sdrf_pipelines/converters/openms/__init__.py
src/sdrf_pipelines/converters/openms/constants.py
src/sdrf_pipelines/converters/openms/experimental_design.py
src/sdrf_pipelines/converters/openms/modifications.py
src/sdrf_pipelines/converters/openms/openms.py
src/sdrf_pipelines/converters/openms/unimod.py
src/sdrf_pipelines/converters/openms/unimod.xml
src/sdrf_pipelines/converters/openms/utils.py
src/sdrf_pipelines/ols/__init__.py
src/sdrf_pipelines/ols/ols.py
src/sdrf_pipelines/sdrf/__init__.py
src/sdrf_pipelines/sdrf/sdrf.py
src/sdrf_pipelines/sdrf/specification.py
src/sdrf_pipelines/sdrf/validators.py
src/sdrf_pipelines/sdrf/schemas/__init__.py
src/sdrf_pipelines/sdrf/schemas/models.py
src/sdrf_pipelines/sdrf/schemas/registry.py
src/sdrf_pipelines/sdrf/schemas/utils.py
src/sdrf_pipelines/sdrf/schemas/validator.py
src/sdrf_pipelines/sdrf/sdrf-templates/templates.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/affinity-proteomics/1.1.0/affinity-proteomics.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/base/1.1.0/base.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/cell-lines/1.1.0/cell-lines.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/crosslinking/1.1.0/crosslinking.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/dda-acquisition/1.1.0/dda-acquisition.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/dia-acquisition/1.1.0/dia-acquisition.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/human/1.1.0/human.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/immunopeptidomics/1.0.0-dev/immunopeptidomics.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/invertebrates/1.1.0/invertebrates.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/metaproteomics/1.0.0-dev/metaproteomics.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/ms-proteomics/1.1.0/ms-proteomics.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/olink/1.0.0/olink.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/plants/1.1.0/plants.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/scripts/generate_manifest.py
src/sdrf_pipelines/sdrf/sdrf-templates/single-cell/1.0.0/single-cell.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/somascan/1.0.0/somascan.yaml
src/sdrf_pipelines/sdrf/sdrf-templates/vertebrates/1.1.0/vertebrates.yaml
src/sdrf_pipelines/utils/__init__.py
src/sdrf_pipelines/utils/error_codes.py
src/sdrf_pipelines/utils/exceptions.py
src/sdrf_pipelines/utils/manifest.py
src/sdrf_pipelines/utils/utils.py
tests/__init__.py
tests/conftest.py
tests/helpers.py
tests/test_convert_openms.py
tests/test_converters_base.py
tests/test_error_codes.py
tests/test_min_columns.py
tests/test_ols.py
tests/test_ontology.py
tests/test_openms.py
tests/test_programmatic_validation.py
tests/test_schemas_utils.py
tests/test_sdrf.py
tests/test_sdrfchecker.py
tests/test_skip_ontology.py
tests/test_unimod.py
tests/data/README.md
tests/data/sample.sdrf.tsv
tests/data/PXD001819/PXD001819.sdrf.tsv
tests/data/PXD001819/README.md
tests/data/PXD001819/expected_experimental_design.tsv
tests/data/PXD001819/expected_openms.tsv
tests/data/PXD015270/PXD015270-Sample-1.tsv
tests/data/erroneous/example.sdrf.tsv
tests/data/erroneous/sdrf_error.tsv
tests/data/erroneous/PXD000288/PXD000288.sdrf.tsv
tests/data/generic/README.md
tests/data/generic/error.sdrf.tsv
tests/data/generic/quantms_dia_dotd_sample.sdrf
tests/data/generic/quantms_dia_dotd_sample_converted.sdrf
tests/data/reference/README.md
tests/data/reference/MSV000079033/MSV000079033-Blood-Plasma-TMT10.sdrf.tsv
tests/data/reference/MSV000079033/MSV000079033-Blood-Plasma-iTRAQ.sdrf.tsv
tests/data/reference/PDC000113/PDC000113.sdrf.tsv
tests/data/reference/PDC000126/PDC000126.sdrf.tsv
tests/data/reference/PDC000180/PDC000180.sdrf.tsv
tests/data/reference/PXD000612/PXD000612.sdrf.tsv
tests/data/reference/PXD001474/PXD001474.sdrf.tsv
tests/data/reference/PXD002137/PXD002137.sdrf.tsv
tests/data/reference/PXD004684/PXD004684.sdrf.tsv
tests/data/reference/PXD006482/PXD006482.sdrf.tsv
tests/data/reference/PXD008934/PXD008934.sdrf.tsv
tests/data/reference/PXD022661/PXD022661.sdrf.tsv
tests/data/reference/PXD027125/PXD027125.sdrf.tsv
tests/data/reference/PXD030304/PXD030304.sdrf.tsv
tests/data/reference/PXD030598/PXD030598.sdrf.tsv
tests/data/reference/PXD034244/PXD034244.sdrf.tsv
tests/data/reference/PXD038526/PXD038526.sdrf.tsv