--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datasets.xml	Mon Jul 22 12:36:52 2024 +0000
@@ -0,0 +1,64 @@
+<tool id="beacon2_datasets" name="Beacon2 Datasets" version="1.0.0" profile="21.05">
+    <description>Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search datasets
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.dataUseConditions)
+            --dataUseConditions '$advanced_settings.dataUseConditions'
+        #end if
+        #if str($advanced_settings.ontologyModifiers)
+            --ontologyModifiers '$advanced_settings.ontologyModifiers'
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.name)
+            --name '$advanced_settings.name'
+        #end if
+        > datasets_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="--dataUseConditions" optional="true" type="text" label="DATAUSECONDITIONS" value="" help="Data use conditions applying to this dataset, e.g. disease specific research" />
+            <param argument="--ontologyModifiers" optional="true" type="text" label="DATA USE CONDITIONS MODIFIERS" value="" help="Modifiers that further specify the datasets, e.g. coronary artery disease" />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Unique identifier of the dataset" />
+            <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the dataset" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_datasets_query" format="json" label="${tool.name} on ${on_string}: Datasets Query" from_work_dir="datasets_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="datasets" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="identification" value="refvar-668fcf57aee552bc911b966e" />
+            <param name="name" value="The Genome in a Bottle Consortium (GIAB)" />
+            <output name="out_datasets_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Datasets queries the datasets collection in the Beacon database to study the variants or individuals in a populations or groups who belong to the same repository.
+    ]]></help>
+    <expand macro="citations" />
+</tool>