Add Stanza NLP tool and data manager

data_managers/data_manager_stanza_models/.shed.yml

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+name: data_manager_stanza_models
+owner: iuc
+description: Data manager for downloading and installing Stanza language models
+long_description: |
+  This data manager allows Galaxy administrators to download and install Stanza
+  language models for use with the Stanza NLP annotation tool. It supports 80+
+  languages with models for tokenization, POS tagging, lemmatization, dependency
+  parsing, NER, sentiment analysis, and constituency parsing.
+homepage_url: https://stanfordnlp.github.io/stanza/
+remote_repository_url: https://github.com/galaxyproject/tools-iuc
+type: unrestricted
+categories:
+  - Data Managers
+  - Text Manipulation
+  - Natural Language Processing

data_managers/data_manager_stanza_models/README.md

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+# Galaxy Data Manager for Stanza Language Models
+
+This Galaxy data manager downloads and installs Stanza language models for use with the Stanza NLP annotation tool, supporting 80+ languages with neural models trained on Universal Dependencies.
+
+## Features
+
+- **80+ languages**: Comprehensive language support for multilingual NLP
+- **Direct HuggingFace download**: Downloads models directly from HuggingFace without requiring stanza installation
+- **Multiple language installation**: Select and install multiple languages simultaneously
+- **Progress reporting**: Shows download progress for each language model
+- **Duplicate prevention**: Checks existing installations to avoid redundant downloads
+- **Data table integration**: Automatically registers models in Galaxy's data table system
+
+## How It Works
+
+This data manager:
+1. **Connects to HuggingFace**: Downloads default_fast model packages directly from Stanford's HuggingFace repository
+2. **No dependencies**: Uses only Python's `urllib.request` - no stanza installation required
+3. **Extracts models**: Unzips model packages to Galaxy's managed storage
+4. **Registers models**: Updates the `stanza_models.loc` data table for tool access
+5. **Version control**: Downloads models compatible with Stanza 1.11.1
+
+## Supported Languages
+
+The data manager supports **80+ languages** including:
+
+### European Languages
+- **Western**: English, German, French, Spanish, Italian, Portuguese, Dutch
+- **Nordic**: Swedish, Danish, Norwegian (Bokmål/Nynorsk), Finnish
+- **Slavic**: Russian, Ukrainian, Polish, Czech, Slovak, Croatian, Serbian, Bulgarian
+- **Other**: Greek, Hungarian, Romanian, Estonian, Latvian, Lithuanian
+
+### Asian Languages
+- **East Asian**: Chinese (Simplified/Traditional), Japanese, Korean
+- **South Asian**: Hindi, Tamil, Telugu, Marathi, Urdu
+- **Southeast Asian**: Vietnamese, Thai, Indonesian
+- **Middle Eastern**: Arabic, Persian, Hebrew, Turkish
+
+### Other Languages
+- **African**: Afrikaans
+- **Minority**: Basque, Galician, Catalan, Armenian, Georgian
+
+See [Stanza's complete model list](https://stanfordnlp.github.io/stanza/available_models.html) for detailed language coverage.
+
+## Model Details
+
+### Model Type
+- **default_fast**: Memory-efficient models without character-level processing
+- **Neural networks**: Pretrained on Universal Dependencies v2.12 treebanks
+- **Multi-task**: Single package includes tokenization, POS, lemma, parsing, and NER models (where available)
+
+### Model Sizes
+- **Typical size**: 50-200MB per language
+- **Variation**: Depends on language complexity and available training data
+- **Storage**: Models persist in Galaxy's `tool-data/stanza_models/` directory
+
+### Model Components
+Each language package may include:
+- **Tokenization**: Sentence and token segmentation
+- **POS tagging**: Universal POS tags and morphological features
+- **Lemmatization**: Base form reduction
+- **Dependency parsing**: Universal Dependencies syntax
+- **NER**: Named entity recognition (available for subset of languages)
+
+## Installation Process
+
+### Admin Setup
+1. **Install this data manager**: `data_manager_stanza_models`
+2. **Install the Stanza tool**: `stanza_nlp`
+3. **Navigate to Admin → Local Data**
+4. **Select "Stanza Language Models"**
+
+### Model Installation
+1. **Choose languages**: Select checkboxes for desired languages
+2. **Run installation**: Data manager will download and extract models
+3. **Monitor progress**: Download status shown for each language
+4. **Verify installation**: Models appear in the Stanza tool's language dropdown
+
+### Post-Installation
+- Models are immediately available to the Stanza NLP tool
+- No restart required
+- Models persist across Galaxy restarts
+- Multiple installations of the same language are prevented
+
+## Data Table Format
+
+Models are registered in `stanza_models.loc` with this format:
+```
+<lang_code>    <display_name>    <lang_code>    <models_path>
+```
+
+Example:
+```
+en    English    en    /galaxy/tool-data/stanza_models/en
+de    German     de    /galaxy/tool-data/stanza_models/de
+```
+
+## Technical Details
+
+### Download Source
+- **Repository**: https://huggingface.co/stanfordnlp/
+- **Model naming**: `stanza-{lang}` (e.g., `stanza-en`, `stanza-de`)
+- **Version**: Models tagged with `v{resources_version}` from Stanford's resources.json
+
+### Storage Structure
+```
+tool-data/
+└── stanza_models/
+    ├── en/
+    │   └── [English model files]
+    ├── de/
+    │   └── [German model files]
+    └── stanza_models.loc
+```
+
+### Dependencies
+- **Python 3.12**: Standard library only
+- **No stanza package**: Downloads directly from HuggingFace
+- **urllib.request**: For HTTP downloads
+- **zipfile**: For model extraction
+
+## Troubleshooting
+
+### Common Issues
+- **Network connectivity**: Ensure access to huggingface.co
+- **Disk space**: Large language sets require substantial storage
+- **Permissions**: Galaxy must have write access to tool-data directory
+
+### Model Verification
+- Check `stanza_models.loc` for registered models
+- Verify model files exist in expected directories
+- Test with Stanza NLP tool after installation
+
+## Citation
+
+This data manager installs models created by the Stanford NLP Group. Please cite:
+
+```
+Qi, Peng, Yuhao Zhang, Yuhui Zhang, Jason Bolton, and Christopher D. Manning. 
+"Stanza: A Python Natural Language Processing Toolkit for Many Human Languages." 
+In Proceedings of the 58th Annual Meeting of the Association for Computational 
+Linguistics: System Demonstrations, 2020.
+```
+
+## Version History
+
+- **1.11.1.3**: Enhanced duplicate prevention and error handling
+- **1.11.1.2**: Improved download progress reporting
+- **1.11.1.1**: Direct HuggingFace download implementation
+- **1.11.1.0**: Initial release