# HG changeset patch
# User p.lucas
# Date 1644481159 0
# Node ID 97f22e5a417dcaa047d4adfb75e08e87db4ea8ab
# Parent  f4f1a63fed38bed0fe59c2c1bc16158ff1b80718
change [ to ( in help

diff -r f4f1a63fed38 -r 97f22e5a417d varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 08:13:56 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 08:19:19 2022 +0000
@@ -1,37 +1,30 @@
 <tool id="varscan" name="VarScan Readcount" version="1">
     <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 format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
         <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 [1]"/>
         <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read [20]"/>
     </inputs>
-
     <outputs>
         <data name="output" format="vcf"/>
     </outputs>
-
     <help>
-
       command: varscan readcounts --help
 
       Min coverage:   1
       Min base qual:  20
-      USAGE: java -jar VarScan.jar readcounts [pileup] OPTIONS
+      USAGE: java -jar VarScan.jar readcounts pileup_file 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]
-
+        --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>
 </tool>