Mercurial > repos > yukke > samtools_v1_1

changeset 6:7a9c736bc13c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add flagstat
author soh.ishiguro3914@gmail.com
date Fri, 21 Nov 2014 18:04:42 +0900
parents 2d4f69268768
children 64a012fe92e3
files samtools_v1_1.xml
diffstat 1 files changed, 2 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_v1_1.xml	Fri Nov 21 17:56:10 2014 +0900
+++ b/samtools_v1_1.xml	Fri Nov 21 18:04:42 2014 +0900
@@ -3,8 +3,7 @@
     <requirement type="package" version="1.1">samtools</requirement>
   </requirements>
   <description>samtools version 1.1.</description>
-  <command interpreter="samtools index">$inputfile
-  2&gt;&amp;1 </command>
+  <command interpreter="samtools flagstat">$inputfile > $outfile</command>
   <inputs>
     <conditional name="command_type">
       <param name="command_type" type="select" label="Execute samtools command">
@@ -39,7 +38,7 @@
         <param format="bam" name="inputfile" type="data" label="index bam file"/>
       </when>
       <when value="flagstat">
-        <param format="bam" name="inputfile" type="data" label="Report bam stats"/>
+        <data format="txt" name="outfile" metadata_source="inputfile"/>
       </when>
     </conditional>
   </inputs>