# HG changeset patch
# User devteam
# Date 1447263256 18000
# Node ID b77178f66fc3730ca1e55302faee2d754e47c7b9
# Parent  8e534225baa9f92f61711dff8aa6e65f14169dfe
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit a1517c9d22029095120643bbe2c8fa53754dd2b7

diff -r 8e534225baa9 -r b77178f66fc3 cuff_macros.xml
--- a/cuff_macros.xml	Fri Dec 19 11:55:55 2014 -0500
+++ b/cuff_macros.xml	Wed Nov 11 12:34:16 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 8e534225baa9 -r b77178f66fc3 cuffcompare_wrapper.xml
--- a/cuffcompare_wrapper.xml	Fri Dec 19 11:55:55 2014 -0500
+++ b/cuffcompare_wrapper.xml	Wed Nov 11 12:34:16 2015 -0500
@@ -225,12 +225,14 @@
   2                 c               Contained        
   3                 j               New isoform        
   4                 e               A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.        
-  5                 i               A single exon transcript falling entirely with a reference intron        
-  6                 r               Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case        
-  7                 p               Possible polymerase run-on fragment        
-  8                 u               Unknown, intergenic transcript        
-  9                 o               Unknown, generic overlap with reference        
-  10             .               (.tracking file only, indicates multiple classifications)
+  5                 i               A single exon transcript falling entirely with a reference intron
+  6                 o               Generic exonic overlap with a reference transcript
+  7                 p               Possible polymerase run-on fragment  
+  8                 r               Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case  
+  9                 u               Unknown, intergenic transcript
+  10                x               Exonic overlap with reference on the opposite strand
+  11                s               An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)
+  12                .               (.tracking file only, indicates multiple classifications)
     
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