Mercurial > repos > devteam > cuffcompare
changeset 1:6d8ab54229a0 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:37:24 -0400 |
| parents | d0d26169cc2a |
| children | a5674ddf2ad7 |
| files | cuff_macros.xml cuffcompare_wrapper.xml shed_upload.tar.gz |
| diffstat | 3 files changed, 14 insertions(+), 12 deletions(-) [+] |
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--- a/cuff_macros.xml Wed Nov 26 13:54:44 2014 -0500 +++ b/cuff_macros.xml Tue Oct 13 12:37:24 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/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) -------