--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/theta.xml	Mon Jan 20 16:24:45 2025 +0000
@@ -0,0 +1,64 @@
+<tool id="cnvkit_theta" name="CNVkit Theta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Convert segments to THetA2 input file 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 '$input_segmented_file' ./sample.cns &&
+        ln -s '$advanced_settings.reference' ./reference.cnn &&
+        ln -s '$advanced_settings.vcf' ./sample.vcf &&
+        cnvkit.py export theta
+            ./sample.cns
+            #if $advanced_settings.reference
+              --reference ./reference.cnn
+            #end if
+            #if $advanced_settings.vcf
+              --vcf ./sample.vcf
+            #end if
+            #if $advanced_settings.sample_id
+              --sample-id '$advanced_settings.sample_id'
+            #end if
+            #if $advanced_settings.normal_id
+              --normal-id '$advanced_settings.normal_id'
+            #end if
+            #if $advanced_settings.min_variant_depth
+              --min-variant-depth $advanced_settings.min_variant_depth
+            #end if
+            #if $advanced_settings.zygosity_freq
+              --zygosity-freq $advanced_settings.zygosity_freq
+            #end if
+            --output sample.cnv.input
+    ]]></command>
+     <inputs>
+        <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" />
+        <section name="advanced_settings" title="Advanced settings" expanded="false">
+            <param argument="--reference" optional="true" type="data" format="tabular" label="Reference" help="Reference copy number profile (.cnn), or normal-sample bin-level log2 copy ratios (.cnr). Use if the tumor_segment input file does not contain a 'weight' column" />
+            <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF" help="VCF file containing SNVs observed in both the tumor and normal samples. Tumor sample ID should match the `tumor_segment` filename or be specified with sample ID" />
+            <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" />
+            <param argument="--normal-id" optional="true" type="text" label="Normal Id" value="" help="Corresponding normal sample ID in the input VCF" />
+            <param argument="--min-variant-depth" optional="true" type="integer" label="Minimum Variant Depth" min="1" value="20" help="Minimum read depth for a SNP in the VCF to be counted. [Default: 20]" />
+            <param argument="--zygosity-freq" optional="true" type="float" label="Zygosity Frequency" min="0" value="0.25" help="Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]" />
+
+        </section>  
+        </inputs>
+    <outputs>
+        <data name="CNVs_Theta" format="tabular" label="${tool.name} on ${on_string}: CNVs theta file" from_work_dir="sample.cnv.input" />
+    </outputs>
+       <tests>
+        <test expect_num_outputs="1">
+            <param name="input_segmented_file" ftype="tabular" value="tumor.cns" />
+            <output name="CNVs_Theta" file="sample.cnv.input" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input).
+    ]]></help>
+    <expand macro="citations" />
+</tool>
+
+
+
+