# HG changeset patch
# User devteam
# Date 1447263331 18000
# Node ID 986b63735a5e9c0048de36d8e41c88bfc8c52082
# Parent  5d8b9dcaf17d375fd30e9d0e8430045ed62998be
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit a1517c9d22029095120643bbe2c8fa53754dd2b7

diff -r 5d8b9dcaf17d -r 986b63735a5e cuff_macros.xml
--- a/cuff_macros.xml	Fri Dec 19 12:01:59 2014 -0500
+++ b/cuff_macros.xml	Wed Nov 11 12:35:31 2015 -0500
@@ -10,8 +10,8 @@
     <stdio>
         <exit_code range="1:" />
         <exit_code range=":-1" />
-        <regex match="Error:" />
-        <regex match="Exception:" />
+        <regex match="Error" />
+        <regex match="Exception" />
     </stdio>
   </xml>
   <xml name="condition_inputs">
@@ -88,4 +88,4 @@
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
-</macros>
\ No newline at end of file
+</macros>
diff -r 5d8b9dcaf17d -r 986b63735a5e cuffquant_wrapper.xml
--- a/cuffquant_wrapper.xml	Fri Dec 19 12:01:59 2014 -0500
+++ b/cuffquant_wrapper.xml	Wed Nov 11 12:35:31 2015 -0500
@@ -128,7 +128,7 @@
             </param>
             <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
             <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
-            <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" 
+            <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
                 help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" />
             </when>
         </conditional>
@@ -140,7 +140,7 @@
     <tests>
         <test>
             <!--
-                cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam 
+                cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam
             -->
             <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" />
             <repeat name="samples">
@@ -188,7 +188,7 @@
 Cuffquant produces one output file:
 
 1. Transcript expression values in binary format.
-    
+
 -------
 
 **Settings**