--- a/bed.xml	Mon Jan 20 16:28:47 2025 +0000
+++ b/bed.xml	Sat Mar 01 11:48:59 2025 +0000
@@ -27,14 +27,14 @@
             #end if
     ]]></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="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" />
-            <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" />
+            <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
             <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
             <expand macro="sample_sex"/>
             <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" />
-            <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
+            <param argument="--diploid-parx-genome" type="text" label="Diploid Parx Genome" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
         </section>  
         </inputs>
     <outputs>
@@ -42,15 +42,34 @@
     </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" />
             <param name="sample_id" value="SampleID" />
             <param name="sample_sex" value="Female" />
             <output name="CNVs_BED" file="sample.cnv.bed" />
         </test>
     </tests>
     <help><![CDATA[
-        Export the segmented copy number data (from a .cns file) to BED format. 
-        The resulting BED file describes copy number gains and losses across each segment.
+
+Export the segmented copy number data (from a .cns file) to BED format. 
+The resulting BED file describes copy number gains and losses across each segment.
+-----
+
+**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>