--- a/seg.xml	Mon Jan 20 16:31:38 2025 +0000
+++ b/seg.xml	Sat Mar 01 11:56:09 2025 +0000
@@ -14,7 +14,7 @@
             --output sample.cnv.seg
     ]]></command>
      <inputs>
-        <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" />
+        <param name="input_segmented_file" type="data" format="cns" label="Segmented copy ratio data file (cns file)" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
             <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
         </section>  
@@ -24,12 +24,30 @@
     </outputs>
        <tests>
         <test expect_num_outputs="1">
-            <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
+            <param name="input_segmented_file" ftype="cns" value="sample.cns" />
             <output name="CNVs_SEG" file="sample.cnv.seg" />
         </test>
     </tests>
     <help><![CDATA[
         Export the segmented copy number data (from a .cns file) to the standard SEG format. 
+    
+-----
+
+**Segmented log2 ratios (.cns)**
+
+Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
+
+.. csv-table::
+   :header-rows: 0
+
+    "chromosome","start, end: Genomic coordinates of the segment"
+    "gene","Gene(s) overlapping the segment."
+    "log2","Mean log2 ratio of the segment."
+    "probes","Mean log2 ratio of the segment."
+    "depth","Average read depth."
+    "weight","Reliability weight."
+    "p_value","Statistical confidence (lower = more significant)."
+
     ]]></help>
     <expand macro="citations" />
 </tool>