--- a/reference.xml	Mon Jan 20 16:27:42 2025 +0000
+++ b/reference.xml	Sat Mar 01 11:52:50 2025 +0000
@@ -81,7 +81,7 @@
                 </section>
             </when>
             <when value="yes">
-                <param name="input_cnn_file" type="data" format="tabular" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" />
+                <param name="input_cnn_file" type="data" format="cnn" multiple="true" label="Sample Target/antitarget Coverage cnn file" help="" />
                 <section name="advanced_settings" title="Advanced settings" expanded="false">
                     <expand macro="reference_interface" />
                     <expand macro="reference_optional" />
@@ -94,7 +94,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="out_referene_tas" format="tabular" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
+        <data name="out_referene_tas" format="cnn" label="${tool.name} on ${on_string}: TAS-on-target coverage" from_work_dir="ref-tas.cnn" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -106,7 +106,7 @@
                         <param name="fasta" ftype="fasta" value="genome.fasta" />
                     </conditional>
                 </section>
-                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+                <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
                 <section name="disable_some_of_the_bias_corrections">
                     <param name="no_gc" value="1" />
                 </section>
@@ -122,7 +122,7 @@
                         <param name="fasta" value="test_buildid"/>
                     </conditional>
                 </section>
-                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
+                <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn" />
                 <section name="disable_some_of_the_bias_corrections">
                     <param name="no_gc" value="1" />    
                 </section>
@@ -138,7 +138,7 @@
                         <param name="fasta" value="test_buildid"/>
                     </conditional>
                 </section>
-                <param name="input_cnn_file" ftype="tabular" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
+                <param name="input_cnn_file" ftype="cnn" value="tumor.targetcoverage.cnn,test.targetcoverage.cnn" />
                 <section name="disable_some_of_the_bias_corrections">
                     <param name="no_gc" value="1" />
                 </section>
@@ -196,7 +196,32 @@
     chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
     of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
     depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
-        
+    
+-----
+
+**Copy Number Reference Profile (.cnn)**
+
+Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
+
+.. 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) (if applicable)."
+    "log2","Reference log2 ratio (typically 0 for diploid regions)."
+    "depth","Average read depth across control samples."
+    "spread","Variability (standard deviation) of coverage in controls."
+
+-----
+
+**Target Coverage File (e.g., sample.targetcoverage.cnn):**
+
+- **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size).
+
+- **Purpose:** Captures on-target sequencing depth.
+
     ]]></help>
     <expand macro="citations" />
 </tool>