From f7cbefc1f3e1c4feb215cff26dbbf463b6d6e362 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Thu, 7 Jul 2016 12:02:51 +0200
Subject: [PATCH] Update gsummary.xml

rpy seems not available within the Conda packages.
So I add rpy2 in the requirements.

It works for me! I :heart: Conda
---
 tools/stats/gsummary.xml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/tools/stats/gsummary.xml b/tools/stats/gsummary.xml
index 6517badea1c..cd0592e3a5e 100644
--- a/tools/stats/gsummary.xml
+++ b/tools/stats/gsummary.xml
@@ -1,9 +1,17 @@
-<tool id="Summary_Statistics1" name="Summary Statistics" version="1.1.0">
+<tool id="Summary_Statistics1" name="Summary Statistics" version="1.1.1">
   <description>for any numerical column</description>
   <edam_topics>
     <edam_topic>topic_2269</edam_topic>
   </edam_topics>
-  <command interpreter="python">gsummary.py $input $out_file1 "$cond"</command>
+  <requirements>
+    <requirement type="package" version="2.15.1">R</requirement>
+    <requirement type="package">rpy</requirement>
+    <requirement type="package" version="2.7.8">rpy2</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1" level="fatal" />
+  </stdio>
+  <command>ptyhon $__tool_directory__/gsummary.py $input $out_file1 "$cond"</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Summary statistics on" help="Dataset missing? See TIP below"/>
     <param name="cond" size="30" type="text" value="c5" label="Column or expression" help="See syntax below">
@@ -13,10 +21,6 @@
   <outputs>
     <data format="tabular" name="out_file1" />
   </outputs>
-  <requirements>
-    <requirement type="package" version="2.15.1">R</requirement>
-    <requirement type="package">rpy</requirement>
-  </requirements>
   <tests>
     <test>
       <param name="input" value="1.bed"/>