# HG changeset patch
# User p.lucas
# Date 1644496526 0
# Node ID 939dcf9b037458944199ce48e6f5ef3e2626e1db
# Parent  2709a3c1548cda65cf72531ed49712ccbf7c3260
add help

diff -r 2709a3c1548c -r 939dcf9b0374 varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 12:34:34 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:35:26 2022 +0000
@@ -12,4 +12,11 @@
   <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>