--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nexus_basic.xml	Mon Jan 20 16:26:53 2025 +0000
@@ -0,0 +1,33 @@
+<tool id="cnvkit_export_nexus_basic" name="CNVkit Export Nexus Basics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Convert bin-level log2 ratios to Nexus Copy Number "basic" format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_segmented_file' ./sample.cnr &&
+        cnvkit.py export nexus-basic
+            ./sample.cnr
+            --output sample.cnv.tsv
+    ]]></command>
+     <inputs>
+        <param name="input_segmented_file" type="data" format="tabular" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
+        </inputs>
+    <outputs>
+        <data name="CNVs_NexusBasic" format="tabular" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.tsv" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_segmented_file" ftype="tabular" value="sample.cnr" />
+            <output name="CNVs_NexusBasic" file="sample.cnv.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[ 
+        This tool converts CNVkit log2 copy ratio data to the Nexus Copy Number "basic" format, 
+        enabling efficient visualisation and analysis of genomic alterations in Nexus software. 
+        This conversion facilitates downstream interpretation and integration with other genomic data.
+    ]]></help>
+    <expand macro="citations" />
+</tool>