--- a/segment.xml	Mon Jan 20 16:37:32 2025 +0000
+++ b/segment.xml	Sat Mar 01 12:06:19 2025 +0000
@@ -50,7 +50,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="filename" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
+        <param name="filename" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
         <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
             <expand macro="additionally_SNP_process" />
         </section>
@@ -59,11 +59,11 @@
         </section>
     </inputs>
     <outputs>
-        <data name="out_sample_segment" format="tabular" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
+        <data name="out_sample_segment" format="cns" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="filename" ftype="tabular" value="tumor.cnr" />
+            <param name="filename" ftype="cnr" value="tumor.cnr" />
             <section name="advanced_settings">
                 <param name="method" value="hmm" />
                 <param name="threshold" value="2" />
@@ -81,6 +81,41 @@
          
          Segmented log2 ratios (.cns) output file contains those columns
           chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
+    
+-----
+
+**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)."
+
+-----
+
+**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>