Add co-occurrence analysis tool#8002
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- Analyzes word co-occurrence relationships from NLP-annotated JSON - Multiple methods: sentence-level, sliding window, dependency-based - Works with spaCy, Stanza, or CoreNLP JSON output - Flexible filtering: POS tags, stop words, custom stop word lists - Term representation options: lemma, surface form, or lowercased - Output formats: TSV pair list and optional co-occurrence matrix - Pure Python implementation with no external dependencies - Comprehensive tests and documentation - Enables downstream network analysis and visualization Tool: cooccurrence_analysis (v1.0.0+galaxy0) Categories: Text Manipulation, Natural Language Processing Citation: Manning & Schütze - Foundations of Statistical NLP
- Analyzes word co-occurrence patterns from spaCy/Stanza JSON output - Supports both span-based and sentence-based co-occurrence analysis - Generates tabular output with co-occurrence frequencies and distances - Works with JSON output from both spaCy and Stanza NLP tools Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
- Analyzes word co-occurrence patterns from spaCy/Stanza JSON output - Supports both span-based and sentence-based co-occurrence analysis - Generates tabular output with co-occurrence frequencies and distances - Works with JSON output from both spaCy and Stanza NLP tools Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
bgruening
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May 20, 2026
| </assert_contents> | ||
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| </test> | ||
| <test expect_num_outputs="1"> |
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can we have one of those tests with all two outputs?
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Regarding the cooccurrence.py source: This implements standard co-occurrence algorithms from computational linguistics (sentence-level, sliding window, dependency-based). The implementation is original code written specifically for Galaxy to process spaCy/Stanza JSON outputs. The algorithms themselves are textbook NLP methods. |
- Update profile from 21.05 to 24.1 - Remove macros.xml and inline version - Fix repository URL to point to IUC repository - Convert test syntax to new conditional format - Add ftype attributes to test outputs - Add test with both outputs (pairs + matrix) - Add license comment to Python script
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Addressed all review comments |
Co-occurrence is a custom Galaxy tool without upstream project, so homepage_url should point to tools-iuc repository
Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
RZ9082
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May 21, 2026
- Updated homepage_url and remote_repository_url to specific tool directory - Fixed has_n_rows -> has_n_lines assertion - (Other suggestions already implemented: conditional syntax, test with both outputs, macros inlined) Co-Authored-By: Claude Sonnet 4 <noreply@anthropic.com>
bgruening
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May 22, 2026
bgruening
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May 22, 2026
bgruening
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May 22, 2026
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Two last comments and suggestions :)
Thanks @ksuderman
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
bgruening
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Jun 7, 2026
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Deployment status: success https://github.com/galaxyproject/tools-iuc/actions/runs/27089306313 |
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