# HG changeset patch
# User devteam
# Date 1487524181 18000
# Node ID 6dc45faebc1d41afdd5acffea0336c5ef90c0857
# Parent  b2ee2bef1926e9af44f1fead69f90c365f0d8860
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

diff -r b2ee2bef1926 -r 6dc45faebc1d cuff_macros.xml
--- a/cuff_macros.xml	Tue Feb 07 18:40:42 2017 -0500
+++ b/cuff_macros.xml	Sun Feb 19 12:09:41 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 b2ee2bef1926 -r 6dc45faebc1d cuffquant_wrapper.xml
--- a/cuffquant_wrapper.xml	Tue Feb 07 18:40:42 2017 -0500
+++ b/cuffquant_wrapper.xml	Sun Feb 19 12:09:41 2017 -0500
@@ -1,13 +1,12 @@
-<tool id="cuffquant" name="Cuffquant" version="@VERSION@.0">
+<tool id="cuffquant" name="Cuffquant" version="@VERSION@.1">
     <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
     <description>Precompute gene expression levels</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
-    <command>
+    <command detect_errors="aggressive"><![CDATA[
         cuffquant
             --no-update-check
             --num-threads=\${GALAXY_SLOTS:-4}
@@ -51,7 +50,7 @@
             '$gtf_input'
             #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
             '$samplestring'
-    </command>
+    ]]></command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
             help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>
diff -r b2ee2bef1926 -r 6dc45faebc1d tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 07 18:40:42 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>