--- a/theta.xml	Mon Jan 20 16:24:45 2025 +0000
+++ b/theta.xml	Sat Mar 01 11:53:33 2025 +0000
@@ -33,12 +33,12 @@
             --output sample.cnv.input
     ]]></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,cnr" label="Segmented copy ratio data file (cns file)" help="" />
         <section name="advanced_settings" title="Advanced settings" expanded="false">
-            <param argument="--reference" optional="true" type="data" format="tabular" label="Reference" help="Reference copy number profile (.cnn), or normal-sample bin-level log2 copy ratios (.cnr). Use if the tumor_segment input file does not contain a 'weight' column" />
+            <param argument="--reference" optional="true" type="data" format="cnn" label="Reference" help="Reference copy number profile (.cnn), or normal-sample bin-level log2 copy ratios (.cnr). Use if the tumor_segment input file does not contain a 'weight' column" />
             <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF" help="VCF file containing SNVs observed in both the tumor and normal samples. Tumor sample ID should match the `tumor_segment` filename or be specified with sample ID" />
-            <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="--normal-id" optional="true" type="text" label="Normal Id" value="" help="Corresponding normal sample ID in the input VCF" />
+            <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="--normal-id" type="text" label="Normal Id" help="Corresponding normal sample ID in the input VCF" />
             <param argument="--min-variant-depth" optional="true" type="integer" label="Minimum Variant Depth" min="1" value="20" help="Minimum read depth for a SNP in the VCF to be counted. [Default: 20]" />
             <param argument="--zygosity-freq" optional="true" type="float" label="Zygosity Frequency" min="0" value="0.25" help="Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]" />
 
@@ -49,12 +49,48 @@
     </outputs>
        <tests>
         <test expect_num_outputs="1">
-            <param name="input_segmented_file" ftype="tabular" value="tumor.cns" />
+            <param name="input_segmented_file" ftype="cns" value="tumor.cns" />
             <output name="CNVs_Theta" file="sample.cnv.input" />
         </test>
     </tests>
     <help><![CDATA[
-        Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input).
+        
+Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input).
+   
+-----
+
+**Copy Number Reference Profile (.cnn)**
+
+Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
+
+.. 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) (if applicable)."
+    "log2","Reference log2 ratio (typically 0 for diploid regions)."
+    "depth","Average read depth across control samples."
+    "spread","Variability (standard deviation) of coverage in controls."
+
+-----
+
+**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>