# HG changeset patch
# User p.lucas
# Date 1644480629 0
# Node ID 1ef844ef84aa1b9dc9a73b6bc1c025754ba5e34c
# Parent  7d7d2806583d84f7faaa1f44720515bc1cbea57c
Try fix bug to install tool

diff -r 7d7d2806583d -r 1ef844ef84aa varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 08:02:44 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 08:10:29 2022 +0000
@@ -5,15 +5,6 @@
         <requirement type="package" version="2.4.4">varscan</requirement>
     </requirements>
 
-    <stdio>
-        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
-        <regex match=".*" source="both" level="log" description="tool progress"/>
-    </stdio>
-
-    <version_command><![CDATA[
-varscan 2>&1 | head -n 1
-    ]]></version_command>
-
     <command><![CDATA[
         varscan readcounts ${input} --min-coverage ${min_cov} --min-base-qual ${min_base_qual} --output-file ${output}
     ]]></command>
@@ -30,22 +21,18 @@
 
     <help>
 
-command: varscan readcounts --help
+      command: varscan readcounts --help
 
-Min coverage:   1
-Min base qual:  20
-USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
-        OPTIONS:
+      Min coverage:   1
+      Min base qual:  20
+      USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
+      OPTIONS:
         --variants-file A list of variants at which to report readcounts
         --output-file   Output file to contain the readcounts
         --min-coverage  Minimum read depth at a position to make a call [1]
         --min-base-qual Minimum base quality at a position to count a read [20]
 
     </help>
-
-    <citations>
-        <citation type="doi">10.1101/gr.129684.111</citation>
-    </citations>
 </tool>