# HG changeset patch
# User p.lucas
# Date 1644496592 0
# Node ID 221cdb2901f3bbcf5d9bbdd963fda49773d57d89
# Parent  939dcf9b037458944199ce48e6f5ef3e2626e1db
add first option

diff -r 939dcf9b0374 -r 221cdb2901f3 varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 12:35:26 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:36:32 2022 +0000
@@ -4,10 +4,11 @@
     <requirement type="package" version="2.4.4">varscan</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    varscan readcounts '${input}' --output-file '${output}'
+    varscan readcounts '${input}' --min-coverage '${min_cov}' --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)"/>		  
   </inputs>
   <outputs>
     <data name="output" format="vcf"/>