Mercurial > repos > jeltje > samtools_1_18_mpileup

changeset 5:ab1f85b31fe9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jeltje
date Mon, 12 Jan 2015 14:52:17 -0500
parents 117867d6f99e
children 6757453c6af9
files samtools_flagstat.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_flagstat.xml	Mon Jan 12 14:50:13 2015 -0500
+++ b/samtools_flagstat.xml	Mon Jan 12 14:52:17 2015 -0500
@@ -2,11 +2,12 @@
   <requirements>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
-  <description>provides simple stats on BAM files</description>
-  <command>samtools flagstat "$input1" > "$output1"
+  <description>creates mpileup for VarScan2</description>
+  <command>samtools flagstat "$input1" "$input2" > "$output1"
   </command>
   <inputs>
     <param name="input1" type="data" format="bam" label="BAM File" />
+    <param name="input2" type="data" format="bam" label="BAM File" />
   </inputs>
   <outputs>
     <data name="output1" format="txt" />