--- a/facets_analysis.xml	Sun Oct 05 00:55:34 2025 +0000
+++ b/facets_analysis.xml	Sun Oct 05 18:42:30 2025 +0000
@@ -13,6 +13,7 @@
             --output_summary '$output_summary'
             --output_spider '$output_spider'
             --output_plots '$output_plots'
+            --output_vcf '$output_vcf'
             --cval $cval
             --min_nhet $min_nhet
             --snp_nbhd $snp_nbhd
@@ -21,7 +22,8 @@
     <inputs>
         <param name="pileup" type="data" format="tabular.gz" label="FACETS Pileup File" help="Output from the 'SNP Pileup for FACETS' tool."/>
         
-        <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)" help="Higher values lead to fewer segments (less sensitive). Lower values are more sensitive."/>
+        <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)"
+               help="Higher values lead to fewer segments (less sensitive). Lower values are more sensitive. For dense data (e.g., from WGS), higher values like 400-800 are recommended."/>
         <param name="min_nhet" type="integer" value="25" label="Minimum number of heterozygous SNPs per segment" help="Ensures that segments are supported by sufficient allelic information."/>
         
         <param name="gbuild" type="select" label="Genome Build">
@@ -39,6 +41,7 @@
         <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
         <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
         <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
+        <data name="output_vcf" format="vcf" label="FACETS CNV calls (VCF) on ${on_string}"/>
 
     </outputs>
     <tests>
@@ -48,6 +51,7 @@
             <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
             <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
             <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
+            <output name="output_vcf" file="test_sample_01.cnv.vcf" ftype="vcf" />
         </test>
     </tests>
     <help><![CDATA[
@@ -55,10 +59,13 @@
 
         This tool runs the `FACETS` R package to perform allele-specific copy number and clonal heterogeneity analysis. It takes the compressed pileup file generated by the "SNP Pileup for FACETS" tool as its primary input.
 
-        The main outputs are:
-        - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN), purity, and ploidy.
-        - A **Summary file** containing the main estimated parameters for the sample (purity, ploidy, etc.).
-        - A **Plots file (PDF)** with standard FACETS visualizations for quality control and interpretation.
+        **Outputs**
+
+        - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN).
+        - A **Summary file** with the main estimated parameters (purity, ploidy, etc.).
+        - A **CNV calls file (VCF)** listing the detected copy number events in a standard VCF format.
+        - A **Plots file (PNG)** with an enhanced visualization of the genome-wide results, including a legend for copy number states.
+        - A **Spider Plot (PNG)** for diagnosing the quality of the purity/ploidy model fit.
     ]]></help>
     <expand macro="citations"/>
 </tool>
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