diff bwa-mem.xml @ 6:09a7281d24c5 draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty

--- a/bwa-mem.xml	Tue Jul 21 13:51:02 2015 -0400
+++ b/bwa-mem.xml	Tue Jul 21 14:12:49 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -9,9 +9,7 @@
     <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
     <requirement type="package" version="1.1">samtools</requirement>
   </requirements>
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+  <expand macro="stdio" />
   <command>
     #set $reference_fasta_filename = "localref.fa"
 
@@ -291,7 +289,9 @@
   </inputs>
 
   <outputs>
-    <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"/>
+    <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
+      <expand macro="dbKeyActionsBwaMem" />
+    </data>
   </outputs>
 
   <tests>