changeset 1:8fb10700729b draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/cuff_macros.xml	Wed Nov 26 14:02:38 2014 -0500
+++ b/cuff_macros.xml	Tue Oct 13 12:38:32 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>

--- a/cuffquant_wrapper.xml	Wed Nov 26 14:02:38 2014 -0500
+++ b/cuffquant_wrapper.xml	Tue Oct 13 12:38:32 2015 -0400
@@ -163,8 +163,8 @@
 
 Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing.  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**
@@ -173,7 +173,7 @@
 
 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/cuffquant/
 
 ------