--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf.xml	Mon Jan 20 16:31:16 2025 +0000
@@ -0,0 +1,64 @@
+<tool id="cnvkit_export_vcf" name="CNVkit Export VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Converts the Segmented copy ratio data file (*.cns) file into VCF file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[  
+        ln -s '$input_segmented_file' ./sample.cns &&
+        ln -s '$advanced_settings.cnr' ./sample.cnr &&
+        cnvkit.py export vcf
+            ./sample.cns
+            #if $advanced_settings.cnr
+              --cnr ./sample.cnr
+            #end if
+            #if $advanced_settings.sample_id
+              --sample-id '$advanced_settings.sample_id'
+            #end if
+            #if $advanced_settings.ploidy
+              --ploidy $advanced_settings.ploidy
+            #end if
+            #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
+              --sample-sex '$advanced_settings.sample_sex'
+            #end if
+            $advanced_settings.male_reference  
+            --output sample.cnv.vcf
+            #if $advanced_settings.diploid_parx_genome
+              --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
+            #end if
+    ]]></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="--cnr" optional="true" type="data" format="tabular" label="Bin-level copy ratios (cnr)" help="" />
+            <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="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
+            <expand macro="sample_sex"/>
+            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
+            <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
+        </section>  
+        </inputs>
+    <outputs>
+        <data name="CNVs_VCF" format="vcf" label="${tool.name} on ${on_string}: CNVs VCF file" from_work_dir="sample.cnv.vcf" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
+            <param name="sample_id" value="SampleID" />
+            <param name="sample_sex" value="Female" />
+            <output name="CNVs_VCF" file="sample.cnv.vcf" ftype="vcf" lines_diff="2" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format. 
+        The resulting VCF file describes copy number gains and losses across each segment and contains 
+        INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+
+
+