diff cuffcompare_wrapper.xml @ 1:6d8ab54229a0 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/cuffcompare_wrapper.xml	Wed Nov 26 13:54:44 2014 -0500
+++ b/cuffcompare_wrapper.xml	Tue Oct 13 12:37:24 2015 -0400
@@ -155,8 +155,8 @@
 
 Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). 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**
@@ -165,7 +165,7 @@
 
 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#cuffcompare
+.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/
 
 ------
 
@@ -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)
     
 -------