# HG changeset patch
# User devteam
# Date 1487524157 18000
# Node ID 6562753c6bdcedcf25e046b90226a3247e23ac24
# Parent  96c4d0e185462f929c35a3fe4d21a77fdc11ce2b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

diff -r 96c4d0e18546 -r 6562753c6bdc cuff_macros.xml
--- a/cuff_macros.xml	Tue Feb 07 18:39:51 2017 -0500
+++ b/cuff_macros.xml	Sun Feb 19 12:09:17 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 96c4d0e18546 -r 6562753c6bdc gffread.xml
--- a/gffread.xml	Tue Feb 07 18:39:51 2017 -0500
+++ b/gffread.xml	Sun Feb 19 12:09:17 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="gffread" name="gffread" version="@VERSION@.0">
+<tool id="gffread" name="gffread" version="@VERSION@.1">
     <description>Filters and/or converts GFF3/GTF2 records</description>
     <macros>
         <import>cuff_macros.xml</import>
@@ -48,8 +48,7 @@
         </xml>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
     #if $reference_genome.source == 'history':
         ln -s '$reference_genome.genome_fasta' genomeref.fa &&
diff -r 96c4d0e18546 -r 6562753c6bdc tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 07 18:39:51 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="87f239da61af" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>