--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/facets_analysis.xml	Fri Oct 03 23:59:36 2025 +0000
@@ -0,0 +1,60 @@
+<tool id="facets_analysis" name="FACETS Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Performs allele-specific copy number analysis from a pileup file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '${__tool_directory__}/facets_analysis.R'
+            --pileup '$pileup'
+            --sample_id '$pileup.name'
+            --output_seg '$output_seg'
+            --output_summary '$output_summary'
+            --output_plots '$output_plots'
+            --cval $cval
+            --min_nhet $min_nhet
+            --snp_nbhd $snp_nbhd
+            --gbuild '$gbuild'
+    ]]></command>
+    <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="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">
+            <option value="hg38" selected="true">Human (hg38)</option>
+            <option value="hg19">Human (hg19)</option>
+            <option value="hg18">Human (hg18)</option>
+            <option value="mm10">Mouse (mm10)</option>
+            <option value="mm9">Mouse (mm9)</option>
+        </param>
+        
+        <param name="snp_nbhd" type="integer" value="300" label="SNP neighborhood size (snp.nbhd)" help="Should match the --pseudo-snps distance used to generate the pileup file. Default is 300."/>
+    </inputs>
+    <outputs>
+        <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
+        <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
+        <data name="output_plots" format="pdf" label="FACETS Plots on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
+            <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
+            <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
+            <output name="output_plots" file="test_sample_01.plots.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **What it does**
+
+        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.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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