--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequence.xml	Mon Jul 22 12:33:53 2024 +0000
@@ -0,0 +1,61 @@
+<tool id="beacon2_sequence" name="Beacon2 Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>َQuery for the existence of a specified sequence at a given genomic position</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search sequence
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        --alternateBases '$alternateBases'
+        --referenceBases '$referenceBases'
+        #if str($advanced_settings.referenceName)
+            --referenceName '$advanced_settings.referenceName'
+        #end if
+        #if str($advanced_settings.start)
+            --start $advanced_settings.start
+        #end if
+        #if str($advanced_settings.collectionIds)
+            --collectionIds '$advanced_settings.collectionIds'
+        #end if
+        > sequenced_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <param argument="--alternateBases" type="text" label="Alternate bases" value="" help="" />
+        <param argument="--referenceBases" type="text" label="Reference bases" value="" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
+            <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
+            <param argument="--collectionIds"  optional="true" type="text" label="Collection ID" value="" help="Datasets ID" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_sequence_query" format="json" label="${tool.name} on ${on_string}: Sequence Query" from_work_dir="sequenced_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="10176" />
+            <param name="alternateBases" value="AC" />
+            <param name="referenceBases" value="A" />
+            <output name="out_sequence_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Sequence Queries query for the existence of a specified sequence at a given genomic position. Such queries correspond to the original Beacon queries and are used to match short, precisely defined genomic variants such as SNVs and INDELs.
+    ]]></help>
+    <expand macro="citations" />
+</tool>