Add entity geocoding tool

tools/geocode/.shed.yml

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+name: geocode_entities
+owner: iuc
+description: Geocode named entities from NLP-annotated JSON to GeoJSON
+long_description: |
+  Extracts location entities (GPE, LOC, FAC) from NLP-annotated JSON output
+  (spaCy or Stanza) and geocodes them using Nominatim (OpenStreetMap). Produces
+  GeoJSON output viewable with Galaxy's OpenLayers visualization plugin, plus
+  a tabular summary of geocoded locations with coordinates and mention counts.
+homepage_url: https://github.com/ksuderman/galaxy_tools_geocode
+remote_repository_url: https://github.com/ksuderman/galaxy_tools_geocode
+type: unrestricted
+categories:
+  - Text Manipulation
+  - Natural Language Processing

tools/geocode/README.md

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+# Galaxy Wrapper for Named Entity Geocoding
+
+This Galaxy tool extracts location-type named entities from NLP-annotated JSON and geocodes them to geographic coordinates using Nominatim (OpenStreetMap), enabling interactive map visualization and spatial analysis of text corpora.
+
+## Features
+
+- **Entity type selection**: Geocode GPE, LOC, FAC, and ORG entities from NER output
+- **Dual output formats**: GeoJSON for map visualization and TSV for analysis
+- **Interactive maps**: GeoJSON viewable directly in Galaxy via OpenLayers plugin
+- **Flexible geocoding**: Public OpenStreetMap API or custom Nominatim instances
+- **Deduplication**: Automatically handles duplicate entity mentions
+- **No dependencies**: Pure Python implementation using only `urllib.request`
+
+## Requirements
+
+- **Input**: JSON output from Galaxy NLP tools (spaCy, Stanza, or CoreNLP) with NER annotations
+- **No dependencies**: No external Python packages or model downloads required
+
+## Entity Types Supported
+
+| Type | Description | Geocoding Success Rate |
+|---|---|---|
+| **GPE** | Geo-Political Entities (countries, cities, states) | High - most reliable |
+| **LOC** | Non-GPE locations (mountains, rivers, regions) | Good - geographic features |
+| **FAC** | Facilities (buildings, airports, highways) | Variable - depends on specificity |
+| **ORG** | Organizations (may resolve if place-named) | Low - use with caution |
+
+## Input Format
+
+The tool expects JSON input with NER annotations:
+```json
+{
+  "sentences": [
+    {
+      "entities": [
+        {
+          "text": "Paris",
+          "label": "GPE",
+          "start_char": 10,
+          "end_char": 15
+        }
+      ]
+    }
+  ]
+}
+```
+
+## Output Formats
+
+### GeoJSON Output
+Standard GeoJSON FeatureCollection with Point geometries. Each feature includes:
+- `name`: Entity text as found in the document
+- `entity_type`: NER label (GPE, LOC, FAC, ORG)
+- `count`: Number of mentions in the text
+- `display_name`: Full address resolved by Nominatim
+- `coordinates`: [longitude, latitude] for map plotting
+
+**Interactive Visualization**: Viewable directly in Galaxy using the **OpenLayers** plugin for interactive maps.
+
+### Tabular Summary (TSV)
+Tab-separated file with columns:
+- `entity`: Entity name
+- `type`: Entity type (GPE, LOC, FAC, ORG)
+- `latitude`: Decimal degrees
+- `longitude`: Decimal degrees  
+- `count`: Number of mentions
+- `display_name`: Full geocoded address
+
+Results are sorted by mention count (most frequent entities first).
+
+## Nominatim Configuration
+
+### Public OpenStreetMap (Default)
+- Uses the public Nominatim API at `nominatim.openstreetmap.org`
+- **Rate limited**: 1 request per second
+- Suitable for small to medium datasets
+- No setup required
+
+### Custom Nominatim Instance
+- Configure your own Nominatim server for high-volume geocoding
+- No rate limiting
+- Better performance for large corpora
+- Self-hosting options:
+  - Docker: `mediagis/nominatim`
+  - Regional extracts from Geofabrik to reduce storage
+  - Local OpenStreetMap data processing
+
+## Example Use Cases
+
+- **Literary geography**: Map fictional and real places mentioned in novels
+- **Historical research**: Visualize geographic references in archival documents
+- **Travel writing analysis**: Track routes and destinations in travel narratives
+- **News analysis**: Map geographic focus of news articles over time
+- **Digital humanities**: Spatial analysis of large text corpora
+
+## Example Workflow
+
+```
+Upload corpus → spaCy NLP (NER, JSON output) → 
+Geocode Entities (GPE + LOC) → GeoJSON → 
+OpenLayers visualization (interactive map)
+```
+
+## Installation
+
+Install this tool from the Galaxy Toolshed: `geocode_entities`
+
+No additional setup required - ready to use with the public Nominatim API.
+
+## Geocoding Notes
+
+- **Disambiguation**: Nominatim returns the most likely match for ambiguous place names
+- **Accuracy**: Results depend on entity recognition quality and Nominatim's coverage
+- **Rate limits**: Public API is limited to 1 req/sec; consider self-hosting for large datasets
+- **Coverage**: Best for well-known places; may fail on very local or historical place names
+
+## Citation
+
+This tool uses OpenStreetMap data via the Nominatim geocoding service. Please cite:
+
+```
+OpenStreetMap contributors. OpenStreetMap. 2024. 
+https://www.openstreetmap.org
+```
+
+## Version History
+
+- **1.0.0+galaxy1**: Initial release with GeoJSON output and OpenLayers integration
+- **1.0.0+galaxy0**: Beta release