--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv.xml	Mon Jul 22 12:34:00 2024 +0000
@@ -0,0 +1,82 @@
+<tool id="beacon2_cnv" name="Beacon2 CNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Retrieve the copy number varients from genomicVariations collection from the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[    
+        beacon2-search cnv
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.variantInternalId)
+            --variantInternalId '$advanced_settings.variantInternalId'
+        #end if
+        #if str($advanced_settings.analysisId)
+            --analysisId '$advanced_settings.analysisId'
+        #end if
+        #if str($advanced_settings.individualId)
+            --individualId '$advanced_settings.individualId'
+        #end if
+        #if str($advanced_settings.start)
+            --start $advanced_settings.start
+        #end if
+        #if str($advanced_settings.end)
+            --end $advanced_settings.end
+        #end if
+        #if str($advanced_settings.chromosome)
+            --chromosome '$advanced_settings.chromosome'
+        #end if
+        #if str($advanced_settings.variantStateId)
+            --variantStateId '$advanced_settings.variantStateId'
+        #end if
+        #if str($advanced_settings.variantState)
+            --variantState '$advanced_settings.variantState'
+        #end if
+        #if str($advanced_settings.sequenceId)
+            --sequenceId '$advanced_settings.sequenceId'
+        #end if
+        > cnv_query_findings.json
+    ]]></command>
+    <expand macro="configfile"/>
+    <inputs>
+        <expand macro="Connection_to_MongoDB" />
+        <expand macro="Database_Configuration" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--variantInternalId" optional="true" type="text" label="VARIANT INTERNAL ID" value="" help="E.g. 11:52900000-134452384:DEL" />
+            <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" />
+            <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="" />
+            <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
+            <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" />
+            <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" />
+            <param argument="--variantStateId" optional="true" type="text" label="VARIANT STATE ID" value="" help="E.g EFO:0030067" />
+            <param argument="--variantState" optional="true" type="text" label="VARIANT STATE" value="" help="E.g. copy number loss" />
+            <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="cnv" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="chromosome" value="1" />
+            <param name="start" value="243618689" />
+            <param name="end" value="243620819" />
+            <param name="variantStateId" value="EFO:0030068" />
+            <output name="out_cnv_query">
+                <assert_contents><has_text_matching expression="_id"/></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon CNV Queries are supposed to return matches of any copy number variants with at least partial overlap of the input parameters
+    ]]></help>
+    <expand macro="citations" />
+</tool>