--- a/scatter.xml	Mon Jan 20 16:40:44 2025 +0000
+++ b/scatter.xml	Sat Mar 01 12:04:46 2025 +0000
@@ -72,7 +72,7 @@
             #end if
     ]]></command>
     <inputs>
-        <param name="input_cnr_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
+        <param name="input_cnr_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
             <expand macro="scatter_optional" />
             <section name="plot_aesthetics" title="Plot aesthetics" expanded="false">
@@ -88,7 +88,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_cnr_file" ftype="tabular" value="tumor.cnr" />
+            <param name="input_cnr_file" ftype="cnr" value="tumor.cnr" />
             <section name="advanced_settings">
                 <section name="additional_SNP_allelic_process">
                     <param name="zygosity_freq" value="0.25" />
@@ -105,6 +105,41 @@
     <help><![CDATA[
         Plot bin-level log2 coverages and segmentation calls together. Without any further arguments,
         this plots the genome-wide copy number in a form familiar to those who have used array CGH.
+
+-----
+
+**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>