# HG changeset patch
# User devteam
# Date 1487524169 18000
# Node ID f5b2ee725d3401dbc1c9ce1b596a4694c05cc75e
# Parent  f8fdf50e0b3bb75c9face1957f1a368d0dc21efb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

diff -r f8fdf50e0b3b -r f5b2ee725d34 cuff_macros.xml
--- a/cuff_macros.xml	Tue Feb 07 18:40:18 2017 -0500
+++ b/cuff_macros.xml	Sun Feb 19 12:09:29 2017 -0500
@@ -8,14 +8,6 @@
     </requirements>
   </xml>
 
-  <xml name="stdio">
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error" />
-        <regex match="Exception" />
-    </stdio>
-  </xml>
   <xml name="condition_inputs">
     <!-- DEFAULT : use BAM/SAM files -->
     <conditional name="in_type">
diff -r f8fdf50e0b3b -r f5b2ee725d34 cuffnorm_wrapper.xml
--- a/cuffnorm_wrapper.xml	Tue Feb 07 18:40:18 2017 -0500
+++ b/cuffnorm_wrapper.xml	Sun Feb 19 12:09:29 2017 -0500
@@ -1,12 +1,11 @@
-<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1">
+<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.2">
     <description>Create normalized expression levels</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
-    <command>
+    <command detect_errors="aggressive">
         cuffnorm
             --no-update-check
             --num-threads="\${GALAXY_SLOTS:-4}"
diff -r f8fdf50e0b3b -r f5b2ee725d34 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 07 18:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="cufflinks" version="2.2.1">
-        <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>