--- a/jtv.xml	Mon Jan 20 16:33:00 2025 +0000
+++ b/jtv.xml	Sat Mar 01 11:50:29 2025 +0000
@@ -13,7 +13,7 @@
             --output sample.cnv.jtv
     ]]></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" label="Log2 Copy Ratio Data File" help="The output of the CNVkit 'fix' sub-command" />
         </inputs>
     <outputs>
         <data name="CNVs_cdt" format="jtv" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.jtv" />
@@ -27,6 +27,25 @@
     <help><![CDATA[ 
         This tool converts CNVkit log2 copy ratio data to Java TreeView's native format (.jtv), 
         enabling easy visualisation and clustering analysis with preserved settings for seamless data exploration.
+
+-----
+
+**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>