--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/runs.xml	Mon Jul 22 12:37:26 2024 +0000
@@ -0,0 +1,86 @@
+<tool id="beacon2_runs" name="Beacon2 Runs" version="1.0.0" profile="21.05">
+    <description>Query the runs 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 runs
+        --db-host '$db_host'
+        --db-port $db_port
+        --database '$database'
+        --collection '$collection'
+        --advance-connection
+        --db-auth-config '$credentials' 
+        #if str($advanced_settings.identification)
+            --identification '$advanced_settings.identification'
+        #end if
+        #if str($advanced_settings.individualId)
+            --individualId '$advanced_settings.individualId'
+        #end if
+        #if str($advanced_settings.libraryLayout)
+            --libraryLayout '$advanced_settings.libraryLayout'
+        #end if
+        #if str($advanced_settings.librarySelection)
+            --librarySelection '$advanced_settings.librarySelection'
+        #end if
+        #if str($advanced_settings.librarySource)
+            --librarySource '$advanced_settings.librarySource'
+        #end if
+        #if str($advanced_settings.libraryStrategy)
+            --libraryStrategy '$advanced_settings.libraryStrategy'
+        #end if
+        #if str($advanced_settings.platform)
+            --platform '$advanced_settings.platform'
+        #end if
+        #if str($advanced_settings.platformModel)
+            --platformModel '$advanced_settings.platformModel'
+        #end if
+        #if str($advanced_settings.runDate)
+            --runDate '$advanced_settings.runDate'
+        #end if
+        > runs_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="--identification" optional="true" type="text" label="ID" value="" help="Run ID" />
+            <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="Reference to the individual ID, e.g. TCGA-AO-A0JJ" />
+            <param argument="--libraryLayout" optional="true" type="text" label="LIBRARY LAYOUT" value="" help="Ontology value for the library layout e.g 'PAIRED', 'SINGLE'" />
+            <param argument="--librarySelection" optional="true" type="text" label="LIBRARY SELECTION" value="" help="Selection method for library preparation, e.g 'RANDOM', 'RT-PCR'" />
+            <param argument="--librarySource" optional="true" type="text" label="LIBRARY SOURCE" value="" help="Ontology value for the source of the sequencing or hybridization library, e.g 'genomic source', 'transcriptomic source'" />
+            <param argument="--libraryStrategy" optional="true" type="text" label="LIBRARY STRATEGY" value="" help="Library strategy, e.g. 'WGS'" />
+            <param argument="--platform" optional="true" type="text" label="PLATFORM" value="" help="General platform technology label where the specific model is not relevant, e.g. Illumina" />
+            <param argument="--platformModel" optional="true" type="text" label="PLATFORM MODEL" value="" help="Ontology value for experimental platform or methodology used, e.g. 'Illumina HiSeq 3000'" />
+            <param argument="--runDate" optional="true" type="text" label="RUN DATE" value="" help="Date at which the experiment was performed" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_runs_query" format="json" label="${tool.name} on ${on_string}: Runs Query" from_work_dir="runs_query_findings.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="database" value="beacon" />
+            <param name="collection" value="runs" />
+            <param name="db_host" value="20.108.51.167" />
+            <param name="platform" value="Illumina " />
+            <param name="platformModel" value="2017-04-30" />
+            <param name="librarySource" value="KAPA library quantification kit" />
+            <param name="libraryLayout" value="PAIRED" />
+            <output name="out_runs_query">
+                <assert_contents>
+                    <has_text_matching expression="_id"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Beacon2 Runs queries the runs collection in the Beacon database for details on procedures used for sequencing a biosample. 
+    ]]></help>
+    <expand macro="citations" />
+</tool>