# HG changeset patch
# User devteam
# Date 1444754299 14400
# Node ID 14a78720e7de15c66a7db925d67c297b32f13af1
# Parent  faa22754dac55654c145d726c5f98f94ea1ea21e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r faa22754dac5 -r 14a78720e7de cuff_macros.xml
--- a/cuff_macros.xml	Wed Nov 26 14:00:49 2014 -0500
+++ b/cuff_macros.xml	Tue Oct 13 12:38:19 2015 -0400
@@ -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 faa22754dac5 -r 14a78720e7de cuffnorm_wrapper.xml
--- a/cuffnorm_wrapper.xml	Wed Nov 26 14:00:49 2014 -0500
+++ b/cuffnorm_wrapper.xml	Tue Oct 13 12:38:19 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.0">
+<tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1">
     <description>Create normalized expression levels</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -92,7 +92,7 @@
             <filter>(include_read_group_files == 'Yes')</filter>
             <filter>(output_format == 'cuffdiff')</filter>
         </data>
-        <data format="text" name="read_groups_info" label="${tool.name} on ${on_string}: Read Groups" from_work_dir="read_groups.info" >
+        <data format="txt" name="read_groups_info" label="${tool.name} on ${on_string}: Read Groups" from_work_dir="read_groups.info" >
             <filter>(include_read_group_files == 'Yes')</filter>
             <filter>(output_format == 'cuffdiff')</filter>
         </data>
@@ -179,8 +179,8 @@
 
 Cuffnorm is part of Cufflinks_. Running Cuffnorm is very similar to running Cuffdiff. Cuffnorm takes a GTF2/GFF3 file of transcripts as input, along with two or more SAM, BAM, or CXB files for two or more samples. It produces a number of output files that contain expression levels and normalized fragment counts at the level of transcripts, primary transcripts, and genes. It also tracks changes in the relative abundance of transcripts sharing a common transcription start site, and in the relative abundances of the primary transcripts of each gene. Tracking the former allows one to see changes in splicing, and the latter lets one see changes in relative promoter use within a gene.. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
 
-.. _Cufflinks: http://cufflinks.cbcb.umd.edu/
-        
+.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
+
 ------
 
 **Know what you are doing**
@@ -189,7 +189,7 @@
 
 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
 
-.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
+.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/
 
 ------