Mercurial > repos > p.lucas > varscan_readcount

changeset 9:221cdb2901f3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add first option
author p.lucas
date Thu, 10 Feb 2022 12:36:32 +0000
parents 939dcf9b0374
children 8ff4f6f5c4f5
files varscan_readcount.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/varscan_readcount.xml	Thu Feb 10 12:35:26 2022 +0000
+++ b/varscan_readcount.xml	Thu Feb 10 12:36:32 2022 +0000
@@ -4,10 +4,11 @@
     <requirement type="package" version="2.4.4">varscan</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    varscan readcounts '${input}' --output-file '${output}'
+    varscan readcounts '${input}' --min-coverage '${min_cov}' --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)"/>		  
   </inputs>
   <outputs>
     <data name="output" format="vcf"/>