# HG changeset patch
# User p.lucas
# Date 1644487174 0
# Node ID 9001935fe8c02c483bbd8ee90334f60072b58657
# Parent  0f875edd8d9194b468c9de231f1352905f6bd78d
Uploaded try to fix error

diff -r 0f875edd8d91 -r 9001935fe8c0 varscan_readcount.xml
--- a/varscan_readcount.xml	Thu Feb 10 09:55:55 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 09:59:34 2022 +0000
@@ -4,21 +4,19 @@
     <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 ${output}
+    varscan readcounts '${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 [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]"/>
+    <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" label="Minimum base quality at a position to count a read (default: 20)"/>
   </inputs>
   <outputs>
     <data name="output" format="vcf"/>
   </outputs>
   <help>
-    COMMAND: varscan readcounts --help
     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 (default: 1)
       --min-base-qual Minimum base quality at a position to count a read (default: 20)