diff varscan_vaf.xml @ 0:0b6ec297a6bc draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf commit ff9426700b78da43ad64bf4905d358ee4986127b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_vaf.xml	Mon Nov 28 21:59:34 2022 +0000
@@ -0,0 +1,55 @@
+<tool id="varscan_vaf" name="Compute VAFs from varscan VCFs" version="0.1">
+    <description />
+    <requirements>
+        <requirement type="package" version="3.7.6">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/varscan_vaf.py
+            --input '$input'
+            --output '$output'
+    ]]></command>
+    <inputs>
+        <param format="vcf" label="VCF file" name="input" type="data"
+               help="a VCF file generated by somatic varscan (normal and tumor genotype),
+                     or having a compatible FORMAT column (9th column)"/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="output" label="VCF with computed VAFs" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="vcf" name="input" value="vcf_1.vcf" />
+            <output file="computed_VAFs_1.vcf" name="output" />
+        </test>
+        <test>
+            <param ftype="vcf" name="input" value="vcf_2.vcf" />
+            <output file="computed_VAFs_2.vcf" name="output" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
++ Computes VAFs in normal and tumor samples.
++ Uses AD field of genotypes (##FORMAT ID=AD), composed of REF and ALT Read depths, separated by a comma.
++ A new genotype field 'VAF" (##FORMAT IF=VAF) is generated
++ VAF = AD(ALT) / (AD(ALT) + AD(REF))
+
+-------
+
+**Inputs**
+
+1. A somatic varscan VCF with AD field in third position.
+2. The AD field must be composed of two integers separated by a comma.
+
+-------
+
+**Output**
+
++ A VCF file
++ A line '##FORMAT=&lt;ID=VAF,Number=R,Type=float,Description="Variant Allele Frequency"&gt;' is added in the header
++ The VAF value is added in both normal and tumor genotype column, as a last field
+
+    </help>
+    <citations />
+</tool>