--- a/nexus_basic.xml	Mon Jan 20 16:26:53 2025 +0000
+++ b/nexus_basic.xml	Sat Mar 01 11:52:29 2025 +0000
@@ -13,21 +13,40 @@
             --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" />
+        <param name="input_segmented_file" type="data" format="cnr,cns" 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" />
+            <param name="input_segmented_file" ftype="cnr" 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.
+
+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.
+    
+-----
+
+**Bin-level log2 ratios (.cnr)**
+
+Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
+
+.. csv-table::
+   :header-rows: 0
+
+    "chromosome","Genomic chromosome (e.g., chr1, chrX)"
+    "start","Start position of the bin."
+    "end","End position of the bin."
+    "gene","Gene name(s) overlapping the bin (if applicable)."
+    "log2","Normalized log2 ratio (sample coverage / reference coverage)."
+    "depth","Average read depth in the bin."
+    "weight","Reliability weight of the bin (higher = more reliable)."
+
     ]]></help>
     <expand macro="citations" />
 </tool>