Mercurial > repos > p.lucas > varscan_readcount

changeset 7:2709a3c1548c draft

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Uploaded minimum xml
author p.lucas
date Thu, 10 Feb 2022 12:34:34 +0000
parents 9001935fe8c0
children 939dcf9b0374
files varscan_readcount.xml
diffstat 1 files changed, 2 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_readcount.xml	Thu Feb 10 09:59:34 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:34:34 2022 +0000
@@ -1,24 +1,15 @@
-<tool id="varscan" name="VarScan Readcount" version="2">
+<tool id="varscan" name="VarScan Readcount" version="2.0">
   <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}'
+    varscan readcounts '${input}' --output-file '${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)"/>
-    <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>
-    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>