--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sex.xml	Fri Sep 29 15:44:27 2023 +0000
@@ -0,0 +1,39 @@
+<tool id="cnvkit_sex" name="CNVkit Sex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators_and_zahra"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_filename_file' ./sample.cnr &&
+        cnvkit.py sex
+            ./sample.cnr      
+            --output gene-sex.txt
+            $male_reference        
+    ]]></command>
+     <inputs>
+        <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr/cnn file" help="Copy number cnn or copy ratio cnr files" />
+        <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
+        </inputs>
+    <outputs>
+        <data name="gene_sex" format="txt" label="${tool.name} on ${on_string}: sample's chromosomal sex" from_work_dir="gene-sex.txt" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
+            <output name="gene_sex" file="gene-sex.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y. 
+        The output is a table of the sample name (derived from the filename), inferred sex (string “Female” or “Male”), 
+        and log2 ratio value of chromosomes X and Y.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+
+
+