# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1415633616 21600
# Node ID 13d81e5226cd8384662cacf540e3932b11c97c08
# Parent  3790e16a0be0a450db351225b73284a9a9c9b38e
Put gene info in Summary Report extra_files_path

diff -r 3790e16a0be0 -r 13d81e5226cd snpEff.xml
--- a/snpEff.xml	Thu Oct 23 05:09:26 2014 -0500
+++ b/snpEff.xml	Mon Nov 10 09:33:36 2014 -0600
@@ -32,7 +32,7 @@
           -interval $intervals
         #end if
         #if $statsFile:
-          -stats $statsFile 
+          -stats snpeff_report
         #end if
         #if $offset.__str__ != 'default':
           ${offset} 
@@ -67,6 +67,9 @@
           $snpDb.genome_version
         #end if
         $input > $snpeff_output 
+        #if $statsFile:
+          &amp;&amp; mkdir $statsFile.extra_files_path  &amp;&amp; cp snpeff_report.genes.txt $statsFile.extra_files_path 
+        #end if
     </command>
     <inputs>
         <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
@@ -220,7 +223,7 @@
                 <when input="outputFormat" value="bedAnn" format="bed" />
             </change_format>
         </data>
-        <data format="html" name="statsFile">
+        <data format="html" name="statsFile" label="{tool.name} on ${on_string} Summary Report" from_work_dir="snpeff_report">
             <filter>generate_stats == True</filter>
         </data>
     </outputs>