# HG changeset patch
# User p.lucas
# Date 1707834690 0
# Node ID ef96ef60f4be949d2fbb71ecc5d1f9c08edab119

Uploaded wrapper

diff -r 000000000000 -r ef96ef60f4be varscan_readcount.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/varscan_readcount.xml	Tue Feb 13 14:31:30 2024 +0000
@@ -0,0 +1,29 @@
+<tool id="varscan" name="VarScan Readcount" version="3">
+  <description>To use varscan readcount tool</description>
+  <requirements>
+    <requirement type="package" version="2.4.4">varscan</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    varscan readcounts '${input}' --min-coverage '${min_cov}' --min-base-qual ${min_base_qual} --output-file '${output}'
+  ]]></command>
+  <inputs>
+    <param name="input" format="pileup" type="data" label="Pileup dataset"/>
+    <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call (default: 1)"/>
+    <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" help="Minimum base quality at a position to count a read (default: 20)"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="vcf"/>
+  </outputs>
+  <help>
+    USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
+
+    OPTIONS:
+
+      --output-file   Output file to contain the readcounts
+
+      --min-coverage  Minimum read depth at a position to make a call (default: 1)
+
+      --min-base-qual Minimum base quality at a position to count a read (default: 20)
+
+  </help>
+</tool>