# HG changeset patch
# User iuc
# Date 1528839063 14400
# Node ID a9b0163b9fab6a0b340f88fcb468d26c9d34075f
# Parent  32705945a08e21d1de14c61989c3c14991f49b3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b

diff -r 32705945a08e -r a9b0163b9fab snpEff.xml
--- a/snpEff.xml	Sat Apr 07 15:45:45 2018 -0400
+++ b/snpEff.xml	Tue Jun 12 17:31:03 2018 -0400
@@ -47,6 +47,9 @@
         #if $statsFile:
           -stats '$statsFile'
         #end if
+        #if $csvStats:
+            -csvStats '$csvFile'
+        #end if
         #if str($offset) != 'default':
           ${offset}
         #end if
@@ -87,7 +90,11 @@
         #if $statsFile:
             &&
             #import os
-            #set $genes_file = str($statsFile) + '.genes.txt'
+            #if $csvStats:
+                #set $genes_file = str($csvFile) + '.genes.txt'
+            #else
+                #set $genes_file = str($statsFile) + '.genes.txt'
+            #end if
             #set $genes_file_name = os.path.split($genes_file)[-1]
             mkdir '$statsFile.files_path' &&
             mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
@@ -120,7 +127,7 @@
             <when value="bed" />
             <when value="bedAnn" />
         </conditional>
-
+        <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
         <conditional name="snpDb">
             <param name="genomeSrc" type="select" label="Genome source">
                 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
@@ -352,9 +359,12 @@
                 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
             </change_format>
         </data>
-        <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">
+        <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
             <filter>generate_stats == True</filter>
         </data>
+        <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
+            <filter>csvStats == True</filter>
+        </data>
     </outputs>
     <tests>
         <test>