--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg.xml	Mon Jan 20 16:31:38 2025 +0000
@@ -0,0 +1,35 @@
+<tool id="cnvkit_export_seg" name="CNVkit Export SEG" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Convert segments to Segment (SEG) format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_segmented_file' ./sample.cns &&
+        cnvkit.py export seg
+            ./sample.cns
+            $advanced_settings.enumerate_chroms  
+            --output sample.cnv.seg
+    ]]></command>
+     <inputs>
+        <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--enumerate-chroms" type="boolean" checked="false" truevalue="--enumerate-chroms" falsevalue="" label="Enumerate Chroms" help="Replace chromosome names with sequential integer IDs" />
+        </section>  
+        </inputs>
+    <outputs>
+        <data name="CNVs_SEG" format="seg" label="${tool.name} on ${on_string}: CNVs SEG file" from_work_dir="sample.cnv.seg" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
+            <output name="CNVs_SEG" file="sample.cnv.seg" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Export the segmented copy number data (from a .cns file) to the standard SEG format. 
+    ]]></help>
+    <expand macro="citations" />
+</tool>