--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/individuals.xml	Mon Jul 22 12:35:16 2024 +0000
@@ -0,0 +1,98 @@
+<tool id="beacon2_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05">
+    <description>Query the individuals collection in the beacon database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        beacon2-search individuals
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.ageGroup)
+            --ageGroup '$advanced_settings.ageGroup'
+        #end if
+        #if str($advanced_settings.diseaseCode)
+            --diseaseCode '$advanced_settings.diseaseCode'
+        #end if
+        #if str($advanced_settings.familyHistory) and $advanced_settings.familyHistory != ""
+            --familyHistory '$advanced_settings.familyHistory'
+        #end if
+        #if str($advanced_settings.severity)
+            --severity '$advanced_settings.severity'
+        #end if
+        #if str($advanced_settings.stage)
+            --stage '$advanced_settings.stage'
+        #end if
+        #if str($advanced_settings.ethnicity)
+            --ethnicity '$advanced_settings.ethnicity'
+        #end if
+        #if str($advanced_settings.geographicOrigin)
+            --geographicOrigin '$advanced_settings.geographicOrigin'
+        #end if
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.assayCode)
+            --assayCode '$advanced_settings.assayCode'
+        #end if
+        #if str($advanced_settings.sex) and $advanced_settings.sex != ""
+            --sex '$advanced_settings.sex'
+        #end if
+        > individuals_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="--ageGroup" optional="true" type="text" label="AGE GROUP" value="" help="age af onset, e.g. Adult 18-65 Years Old" />
+            <param argument="--diseaseCode" optional="true" type="text" label="DISEASE CODE" value="" help="Disease code, Spinocerebellar ataxia 1" />
+            <param argument="--familyHistory" optional="true" type="select" label="FAMILY HISTORY" help="">
+            <option value="true">true</option>
+            <option value="false">false</option>
+            <option value="" selected="True">unknown</option>
+            </param>
+            <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="e.g. Profound" />
+            <param argument="--stage" optional="true" type="text" label="STAGE" value="" help="e.g. acute onset" />
+            <param argument="--ethnicity" optional="true" type="text" label="ETHNICITY" value="" help="e.g. European" />
+            <param argument="--geographicOrigin" optional="true" type="text" label="GEOGRAPHIC ORIGIN" value="" help="e.g. Slovenia" />
+            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Individual identifier (internal ID)" />
+            <param argument="--assayCode" optional="true" type="text" label="ASSAY CODE" value="" help="e.g. Platelets [#/volume] in Blood" />
+            <param argument="--sex" optional="true" type="select" label="SEX" help="">
+            <option value="male">male</option>
+            <option value="female">female</option>
+            <option value="" selected="True">non specific</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_individuals_query" format="json" label="${tool.name} on ${on_string}: Individuals Query" from_work_dir="individuals_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="individuals" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="sex" value="male" />
+            <param name="geographicOrigin" value="United States of America" />
+            <param name="diseaseCode" value="intolerance" />
+            <param name="ethnicity" value="Han Chinese" />
+            <output name="out_individuals_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Individuals queries the individuals collection in the Beacon database for either patients or healthy controls whose details (including phenotypic and clinical) are stored in the repository.
+    ]]></help>
+    <expand macro="citations" />
+</tool>