--- a/breaks.xml	Mon Jan 20 16:29:08 2025 +0000
+++ b/breaks.xml	Sat Mar 01 11:48:14 2025 +0000
@@ -18,8 +18,8 @@
             #end if                    
     ]]></command>
     <inputs>
-        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
-        <param name="input_segment_file" type="data"  format="tabular" label="CN segmentation calls cnn file" help="The output of the CNVkit segment" />
+        <param name="input_filename_file" type="data" format="cnr" label="Bin-Level log2 Ratios/Coverages cnr file" help="The output of the CNVkit fix" />
+        <param name="input_segment_file" type="data"  format="cns" label="CN segmentation calls cns file" help="The output of the CNVkit segment" />
         <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" value="1" help="Minimum number of covered probes to label a gene" />     
     </inputs>
     <outputs>
@@ -27,8 +27,8 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
-            <param name="input_segment_file" ftype="tabular" value="sample.cns" />
+            <param name="input_filename_file" ftype="cnr" value="sample.cnr" />
+            <param name="input_segment_file" ftype="cns" value="sample.cns" />
             <param name="min_probes" value="1" />
             <output name="gene_breaks">
                 <assert_contents><has_text text="chromosome"/></assert_contents>
@@ -43,6 +43,41 @@
        
        The breaks output is a text table of tab-separated values, which is amenable to further processing by 
        scripts and standard Unix tools such as grep, sort, cut and awk. 
+
+-----
+
+**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>