--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/range.xml	Mon Jul 22 12:34:31 2024 +0000
@@ -0,0 +1,73 @@
+<tool id="beacon2_range" name="Beacon2 Range" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Retrieve the genomic variants from the beacon database by specifying start and end positions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search range
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials'
+        --start $start
+        --end $end
+        #if str($advanced_settings.referenceName)
+            --referenceName '$advanced_settings.referenceName'
+        #end if
+        #if str($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 $advanced_settings.variantMaxLength
+        #end if
+        > ranged_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--start" type="integer" label="START" value="" help="Start position" />
+        <param argument="--end" type="integer" label="END" value="" help="End position" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
+            <param argument="--alternateBases"  optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
+            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
+            <param argument="--aminoacidChange"  optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
+            <param argument="--variantMinLength"  optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
+            <param argument="--variantMaxLength"  optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_ranged_query" format="json" label="${tool.name} on ${on_string}: Range Query" from_work_dir="ranged_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="start" value="131836" />
+            <param name="end" value="131837" />
+            <param name="variantType" value="SNP" />
+            <output name="out_ranged_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon Range Queries are supposed to return matches of any variant with at least partial overlap of the sequence range specified by reference_name, start and end parameters
+    ]]></help>
+    <expand macro="citations" />
+</tool>