Mercurial > repos > devteam > cuffcompare
changeset 7:b77178f66fc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:34:16 -0500 |
| parents | 8e534225baa9 |
| children | 1322b73ffe44 |
| files | cuff_macros.xml cuffcompare_wrapper.xml |
| diffstat | 2 files changed, 11 insertions(+), 9 deletions(-) [+] |
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--- 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>
--- 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) -------