Add ZOOMA Galaxy wrapper for column-based API annotation of tabular inputs#747
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Add ZOOMA Galaxy wrapper for column-based API annotation of tabular inputs#747
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Agent-Logs-Url: https://github.com/RECETOX/galaxytools/sessions/1651b5f7-cbd5-452a-bb50-ed22f917bcd4 Co-authored-by: hechth <12066490+hechth@users.noreply.github.com>
Agent-Logs-Url: https://github.com/RECETOX/galaxytools/sessions/1651b5f7-cbd5-452a-bb50-ed22f917bcd4 Co-authored-by: hechth <12066490+hechth@users.noreply.github.com>
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[WIP] Add wrapper for ZOOMA tool web API
Add ZOOMA Galaxy wrapper for column-based API annotation of tabular inputs
Apr 17, 2026
bgruening
reviewed
Apr 17, 2026
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| def query_zooma(query_value, api_url, timeout): | ||
| response = requests.get( |
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maybe implement a retry when blocked by rate-limit?
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| <tool id="zooma" name="ZOOMA annotate" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |||
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please include a profile version
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| <requirements> | ||
| <requirement type="package" version="3.12">python</requirement> | ||
| <requirement type="package" version="2.32.3">requests</requirement> |
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request should bring in a python version, so you can drop the explicit python version
| <param name="api_url" type="text" value="https://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate" label="ZOOMA API URL"> | ||
| <help>Override only if you need a different compatible endpoint.</help> | ||
| </param> | ||
| <param name="timeout" type="integer" value="30" min="1" label="HTTP request timeout (seconds)" /> |
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Not sure this should be offered to a user.
| <help>Override only if you need a different compatible endpoint.</help> | ||
| </param> | ||
| <param name="timeout" type="integer" value="30" min="1" label="HTTP request timeout (seconds)" /> | ||
| <param name="mock_response" type="data" format="json" optional="true" label="Optional mocked JSON response file" help="Optional test/offline map: query term -> list of ZOOMA annotations." /> |
| <param name="input" type="data" format="tabular,csv,tsv" label="Input table" /> | ||
| <param name="has_header" type="boolean" truevalue="--has-header" falsevalue="" checked="true" label="Input file contains a header row" /> | ||
| <param name="query_column" type="data_column" data_ref="input" numerical="false" use_header_names="true" label="Column used for ZOOMA query" /> | ||
| <param name="api_url" type="text" value="https://www.ebi.ac.uk/spot/zooma/v2/api/services/annotate" label="ZOOMA API URL"> |
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this should be hard-coded
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This PR introduces a new Galaxy tool wrapper for ZOOMA that annotates values from a user-selected column in a tabular dataset via the ZOOMA web API and emits a tabular result. It adds a minimal, tool-native implementation aligned with existing
tools/*layout and metadata conventions in this repository.New Galaxy tool:
tools/zoomazooma.xmlwith inputs for:data_column, header-aware)Python API wrapper
zooma.pythat:propertyValue=<value>)Offline/deterministic execution support
Tool packaging metadata and fixtures
macros.xmland.shed.yml.tools/zooma/test-data/:input.tsvmock_response.jsonexpected.tsvWarning
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wheels.galaxyproject.org/home/REDACTED/.planemo/gx_venv_3/bin/python python -m pip install -r requirements.txt --extra-index-url REDACTED(dns block)/home/REDACTED/.planemo/gx_venv_3/bin/python /home/REDACTED/.planemo/gx_venv_3/bin/python /home/REDACTED/.planemo/gx_venv_3/lib/python3.12/site-packages/pip/__pip-REDACTED__.py install --ignore-installed --no-user --prefix /tmp/pip-build-env-8lu_0wz7/overlay --no-warn-script-location --disable-pip-version-check --no-compile --target(dns block)/home/REDACTED/.planemo/gx_venv_3/bin/python /home/REDACTED/.planemo/gx_venv_3/bin/python /home/REDACTED/.planemo/gx_venv_3/lib/python3.12/site-packages/pip/__pip-REDACTED__.py install --ignore-installed --no-user --prefix /tmp/pip-build-env-j7uyg6mi/overlay --no-warn-script-location --disable-pip-version-check --no-compile --target(dns block)www.ebi.ac.uk/home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js(dns block)/usr/bin/python python -(dns block)If you need me to access, download, or install something from one of these locations, you can either: