--- a/cdt.xml	Mon Jan 20 16:29:29 2025 +0000
+++ b/cdt.xml	Sat Mar 01 11:51:21 2025 +0000
@@ -13,20 +13,39 @@
             --output sample.cnv.cdt
     ]]></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="cdt" label="${tool.name} on ${on_string}: CNVs Nexus Basic File" from_work_dir="sample.cnv.cdt" />
     </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_cdt" file="sample.cnv.cdt" />
         </test>
     </tests>
     <help><![CDATA[ 
         This tool converts CNVkit log2 copy ratio data to the CDT format, which is compatible with Java TreeView for visualisation and hierarchical clustering. 
         The conversion enables efficient exploration and interpretation of genomic copy number variations.
+
+-----
+
+**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>