--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene.xml	Mon Jul 22 12:36:40 2024 +0000
@@ -0,0 +1,68 @@
+<tool id="beacon2_gene" name="Beacon2 Gene" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Queries the beacon database and retrieve the genomic variants matching gene symbol</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search gene
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        --geneId $geneId
+        #if str($advanced_settings.alternateBases)
+            --alternateBases '$advanced_settings.alternateBases'
+        #end if
+        #if str($advanced_settings.variantType)
+            --variantType '$advanced_settings.variantType'
+        #end if
+        #if str($advanced_settings.aminoacidChange)
+            --aminoacidChange '$advanced_settings.aminoacidChange'
+        #end if
+        #if str($advanced_settings.variantMinLength)
+            --variantMinLength $advanced_settings.variantMinLength
+        #end if
+        #if str($advanced_settings.variantMaxLength)
+            --variantMaxLength $advanced_settings.variantMaxLength
+        #end if
+        > gene_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--geneId" type="text" label="Gene Id" value="" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--alternateBases"  optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
+            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
+            <param argument="--aminoacidChange"  optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
+            <param argument="--variantMinLength"  optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
+            <param argument="--variantMaxLength"  optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_gene_query" format="json" label="${tool.name} on ${on_string}: Gene Query" from_work_dir="gene_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="genomicVariations" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="geneId" value="OR4F5-LOC729737" />
+            <param name="alternateBases" value="A" />
+            <param name="variantType" value="SNP" />
+            <param name="aminoacidChange" value="." />
+            <output name="out_gene_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        GeneId Queries are in essence a variation of Range Queries in which the coordinates are replaced by the HGNC gene symbol. It is left to the implementation if the matching is done on variants annotated for the gene symbol or if a positional translation is being applied.
+    ]]></help>
+    <expand macro="citations" />
+</tool>