Mercurial > repos > p.lucas > varscan_readcount

changeset 2:1ef844ef84aa draft

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Try fix bug to install tool
author p.lucas
date Thu, 10 Feb 2022 08:10:29 +0000
parents 7d7d2806583d
children f4f1a63fed38
files varscan_readcount.xml
diffstat 1 files changed, 5 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- 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>