Mercurial > repos > joe-usc > ceas
changeset 6:e281a5491a1f draft
planemo upload
| author | joe-usc |
|---|---|
| date | Sun, 20 Nov 2016 23:33:36 -0500 |
| parents | aa2296827914 |
| children | 527a2d26249f |
| files | ceas.xml test-data/H3K36me3.R test-data/log.txt |
| diffstat | 3 files changed, 27 insertions(+), 2 deletions(-) [+] |
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--- a/ceas.xml Sun Nov 20 22:56:39 2016 -0500 +++ b/ceas.xml Sun Nov 20 23:33:36 2016 -0500 @@ -6,7 +6,7 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - ceas -g $gdb -b $bed > $log_output + ceas -g $gdb -b $bed > $log_output 2>&1 ]]></command> <inputs> <param type="data" name="gdb"/>
--- a/test-data/H3K36me3.R Sun Nov 20 22:56:39 2016 -0500 +++ b/test-data/H3K36me3.R Sun Nov 20 23:33:36 2016 -0500 @@ -15,7 +15,7 @@ # span size (gene-centered annotation) = 3000 bp pdf("H3K36me3.pdf",height=11.5,width=8.5) -# 18:35:04 Sun, 20 Nov 2016 +# 20:27:57 Sun, 20 Nov 2016 # # ChIP annotation #
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Sun Nov 20 23:33:36 2016 -0500 @@ -0,0 +1,25 @@ +INFO @ Sun, 20 Nov 2016 20:27:54: +# ARGUMENTS: +# name = H3K36me3 +# gene annotation table = hg19.refGene +# BED file = H3K36me3.bed +# WIG file = None +# extra BED file = None +# ChIP annotation = On +# gene-centered annotation = On +# average profiling = Off +# dump profiles = Off +# re-annotation for genome background (ChIP region annotation) = False +# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp +# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp +# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp +# span size (gene-centered annotation) = 3000 bp +INFO @ Sun, 20 Nov 2016 20:27:54: #1 read the gene table... +INFO @ Sun, 20 Nov 2016 20:27:56: #2 read the bed file of ChIP regions... +INFO @ Sun, 20 Nov 2016 20:27:56: #3 perform gene-centered annotation... +INFO @ Sun, 20 Nov 2016 20:27:57: #4 See H3K36me3.xls for gene-centered annotation! +INFO @ Sun, 20 Nov 2016 20:27:57: #5 read the pre-computed genome bg annotation... +INFO @ Sun, 20 Nov 2016 20:27:57: #6 perform ChIP region annotation... +INFO @ Sun, 20 Nov 2016 20:27:57: #7 write a R script of ChIP region annotation... +/bin/sh: 1: R: not found +INFO @ Sun, 20 Nov 2016 20:27:57: #... cong! See H3K36me3.pdf for the graphical results of CEAS!