Add locuszoom to galaxy visualizations.

client/gulpfile.js

@@ -45,6 +45,7 @@ const INSTALL_PLUGIN_BUILD_IDS = [
     "vitessce",
     "vizarr",
     "vtk",
+    "locuszoom",
 ]; // todo: derive from XML
 
 const args = process.argv.slice(2);

config/plugins/visualizations/locuszoom/config/locuszoom.xml

@@ -0,0 +1,125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="LocusZoom" embeddable="true">
+    <description>LocusZoom Manhattan Plot</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext">gwas_bgzip</test>
+        </data_source>
+    </data_sources>
+    <params>
+        <param required="true">dataset_id</param>
+    </params>
+    <settings>
+        <input>
+            <label>Add tabix file for your primary dataset</label>
+            <help>Can be created with tabix</help>
+            <name>tabix</name>
+            <type>data</type>
+            <extension>gwas_tabix.gz</extension>
+        </input>
+        <input>
+            <label>Select a chromosome</label>
+            <name>chromosome</name>
+            <type>integer</type>
+            <min>1</min>
+            <value>1</value>
+        </input>
+        <input>
+            <label>Select start position</label>
+            <name>start</name>
+            <type>integer</type>
+            <min>1</min>
+            <value>1</value>
+        </input>
+        <input>
+            <label>Select end position</label>
+            <name>end</name>
+            <type>integer</type>
+            <min>1</min>
+            <value>999999</value>
+        </input>
+        <input>
+            <label>Are the p-values in -log10?</label>
+            <name>is_neg_log_pvalue</name>
+            <type>boolean</type>
+            <value>false</value>
+        </input>
+        <input>
+            <label>Column for chromosomes</label>
+            <name>chrom_col</name>
+            <type>integer</type>
+            <value>1</value>
+        </input>
+        <input>
+            <label>Column for positions</label>
+            <name>pos_col</name>
+            <type>integer</type>
+            <value>2</value>
+        </input>
+        <input>
+            <label>Column for reference allele</label>
+            <name>ref_col</name>
+            <type>integer</type>
+            <value>6</value>
+        </input>
+        <input>
+            <label>Column for alternative allele</label>
+            <name>alt_col</name>
+            <type>integer</type>
+            <value>7</value>
+        </input>
+        <input>
+            <label>Column for p-values</label>
+            <name>pvalue_col</name>
+            <type>integer</type>
+            <value>13</value>
+        </input>
+        <input>
+            <label>Column for beta</label>
+            <name>beta_col</name>
+            <type>integer</type>
+            <value>9</value>
+        </input>
+        <input>
+            <label>Column for standard error of beta</label>
+            <name>stderr_beta_col</name>
+            <type>integer</type>
+            <value>10</value>
+        </input>
+    </settings>
+    <requirements>
+        <requirement type="npm" version="0.0.3" package="@galaxyproject/locuszoom"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <tests>
+        <test>
+            <param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/1.gwas_bgzip" ftype="gwas_bgzip" />
+        </test>
+        <test>
+            <param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/1.gwas_tabix.gz" ftype="gwas_tabix.gz" />
+        </test>
+    </tests>
+     <help format="markdown"><![CDATA[
+# What is LocusZoom?
+
+LocusZoom is a specialized tool designed to create interactive Manhattan plots for visualizing results from genome-wide association studies (GWAS).
+It helps researchers explore genetic association signals within specific chromosomal regions.
+
+## Key Features
+
+- **Interactive Manhattan Plots**: Visualize GWAS results with zoom and pan capabilities to focus on genomic regions of interest.
+- **Chromosome-Specific Visualization**: Plots are rendered for one chromosome at a time within a user-specified genomic region.
+- **Tabix-Indexed File Support**: Efficiently handles large datasets by working with tabix-indexed files, enabling fast data retrieval.
+
+This tool is essential for detailed examination of association signals in GWAS, facilitating interpretation of complex genomic data.
+
+The input dataset for GWAS results must have size of at least 64ko. Accepted extenstions are gwas_bgzip for this primary dataset and gwas_tabix.gz for the corresponding tabix.
+
+For more information:
+
+Boughton, A. P. et al. LocusZoom.js: interactive and embeddable visualization of genetic association study results. Bioinformatics (2021) doi:10.1093/bioinformatics/btab186.
+
+    ]]></help>
+</visualization>

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -597,6 +597,10 @@
     <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <!-- GWAS results datatypes to be used with locuszoom visualization plugin -->
+    <datatype extension="gwas_bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <datatype extension="gwas_tabix.gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <!-- -->
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>