Merge pull request galaxyproject#20214 from guerler/chiraviz.000

Migrate ChiraViz

Author: guerler

client/gulpfile.js

@@ -14,7 +14,6 @@ const xml2js = require("xml2js");
  */
 const PLUGIN_BUILD_IDS = [
     "annotate_image",
-    "chiraviz",
     "example",
     "fits_graph_viewer",
     "hyphyvision",
@@ -30,6 +29,7 @@ const INSTALL_PLUGIN_BUILD_IDS = [
     "aceeditor",
     "aladin",
     "alignment",
+    "chiraviz",
     "cytoscape",
     "drawrna",
     "h5web",

config/plugins/visualizations/chiraviz/config/chiraviz.xml

@@ -1,16 +1,53 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
-<visualization name="ChiRAViz">
-    <description>ChiRAViz</description>
+<visualization name="RNA ChiRAViz" embeddable="true">
+    <description>ChiRA tool for chimeric read data</description>
     <data_sources>
         <data_source>
-           <model_class>HistoryDatasetAssociation</model_class>
-           <test type="isinstance" test_attr="datatype" result_type="datatype">binary.ChiraSQLite</test>
-            <to_param param_attr="id">dataset_id</to_param>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext">chira.sqlite</test>
         </data_source>
     </data_sources>
     <params>
-        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+        <param required="true">dataset_id</param>
     </params>
-    <template>chiraviz.mako</template>
+    <requirements>
+        <requirement type="npm" version="0.0.0" package="@galaxyproject/chiraviz"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/script.js" css="dist/main.css" />
+    <tests>
+        <test>
+            <param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/1.chira.sqlite" ftype="chira.sqlite" />
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+# What is RNA ChiRAViz?
+
+**ChiRAViz** is a visualization tool for exploring *chimeric read alignments* using datasets produced by the ChiRA tool, typically in `chira.sqlite` format.
+
+This visualization enables researchers to interactively examine structural variations, fusion transcripts, and other chimeric events identified from RNA-seq data.
+
+## How to Use
+
+1. **Input Dataset**: Select a dataset in `chira.sqlite` format. This should be generated using the ChiRA tool from RNA sequencing data.
+2. **Visualization**: Once the dataset is loaded, you can:
+   - Navigate through detected chimeric junctions.
+   - Inspect fusion evidence, read alignments, and relevant gene annotations.
+   - Interact with graphical views to zoom, filter, and highlight key features.
+
+## Features
+
+- **Interactive Graphs**: Explore chimeric junctions in detail with responsive plots.
+- **Gene Annotations**: Visual cues help correlate fusion sites with gene models.
+- **Efficient Performance**: Supports large datasets with client-side rendering.
+
+## Requirements
+
+Ensure the input dataset has the `.chira.sqlite` extension and includes all necessary metadata from a successful ChiRA analysis run.
+
+---
+
+For more information on the ChiRA pipeline take a look at:
+[https://doi.org/10.1093/gigascience/giaa158](https://doi.org/10.1093/gigascience/giaa158)
+    ]]></help>
 </visualization>