# HG changeset patch
# User nikhil-joshi
# Date 1418126074 18000
# Node ID 012afa77c72458fa56ea3d220ed10a57b3979d27
# Parent d59bf233d184ff390f596ab24beafaa4e02170e3
Uploaded
diff -r d59bf233d184 -r 012afa77c724 README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Tue Dec 09 06:54:34 2014 -0500
@@ -0,0 +1,2 @@
+You can find the CEAS databases here:
+http://liulab.dfci.harvard.edu/CEAS/download.html
diff -r d59bf233d184 -r 012afa77c724 ceas.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas.xml Tue Dec 09 06:54:34 2014 -0500
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+
+ Get stats on ChIP enrichment and infer genes regulated by binding factors
+
+
+ mkdir -p "$pdf_out.files_path" &&
+ cd "$pdf_out.files_path" &&
+
+ ceas
+
+ -g "$refgene_table.fields.path"
+ #if $analysis_files.wig_or_bed == "bed" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
+ -b $chip_bed
+ #end if
+
+ #if $analysis_files.wig_or_bed == "wig" or $analysis_files.wig_or_bed == "both1" or $analysis_files.wig_or_bed == "both2":
+ -w $chip_wig
+ #end if
+
+ #if $analysis_files.wig_or_bed == "both2":
+ --bg
+ #end if
+
+ #if str($extra_bed) != 'None':
+ -e $extra_bed
+ #end if
+
+ #if str($sizes) != "":
+ --sizes=$sizes
+ #end if
+
+ #if str($bisizes) != "":
+ --bisizes=$bisizes
+ #end if
+
+ #if str($span) != "":
+ --span=$span
+ #end if
+
+ #if str($pfres) != "":
+ --pf-res=$pfres
+ #end if
+
+ #if str($reldist) != "":
+ --rel-dist=$reldist
+ #end if
+
+ --name=ceas_out
+
+ 2> /dev/null
+
+ &&
+
+ #if $analysis_files.wig_or_bed != "wig":
+ mv $pdf_out.files_path/ceas_out.xls $annot_out &&
+ #end if
+ mv $pdf_out.files_path/ceas_out.R $r_out &&
+ mv $pdf_out.files_path/ceas_out.pdf $pdf_out &&
+
+ rm -r "$pdf_out.files_path"
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+ (analysis_files['wig_or_bed'] != 'wig')
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+Options:
+ -b BED, --bed=BED BED file of ChIP regions.
+ -w WIG, --wig=WIG WIG file for either wig profiling or genome background
+ annotation. WARNING: --bg flag must be set for genome
+ background re-annotation.
+ -e EBED, --ebed=EBED BED file of extra regions of interest (eg, non-coding
+ regions)
+ -g GDB, --gt=GDB Gene annotation table (eg, a refGene table in sqlite3
+ db format provided through the CEAS web,
+ http://liulab.dfci.harvard.edu/CEAS/download.html).
+ --sizes=SIZES Promoter (also dowsntream) sizes for ChIP region
+ annotation. Comma-separated three values or a single
+ value can be given. If a single value is given, it
+ will be segmented into three equal fractions (ie, 3000
+ is equivalent to 1000,2000,3000), DEFAULT:
+ 1000,2000,3000. WARNING: Values > 10000bp are
+ automatically set to 10000bp.
+ --bisizes=BISIZES Bidirectional-promoter sizes for ChIP region
+ annotation Comma-separated two values or a single
+ value can be given. If a single value is given, it
+ will be segmented into two equal fractions (ie, 5000
+ is equivalent to 2500,5000) DEFAULT: 2500,5000bp.
+ WARNING: Values > 20000bp are automatically set to
+ 20000bp.
+ --bg Run genome BG annotation again. WARNING: This flag is
+ effective only if a WIG file is given through -w
+ (--wig). Otherwise, ignored.
+ --span=SPAN Span from TSS and TTS in the gene-centered annotation.
+ ChIP regions within this range from TSS and TTS are
+ considered when calculating the coverage rates in
+ promoter and downstream, DEFAULT=3000bp
+ --pf-res=PF_RES Wig profiling resolution, DEFAULT: 50bp. WARNING:
+ Value smaller than the wig interval (resolution) may
+ cause aliasing error.
+ --rel-dist=REL_DIST Relative distance to TSS/TTS in wig profiling,
+ DEFAULT: 3000bp
+
+
+
diff -r d59bf233d184 -r 012afa77c724 ceas_tables.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas_tables.loc.sample Tue Dec 09 06:54:34 2014 -0500
@@ -0,0 +1,8 @@
+ce4 C. elegans ce4 /opt/galaxy/tool-data/ceas_tables/ce4.refGene
+ce6 C. elegans ce6 /opt/galaxy/tool-data/ceas_tables/ce6.refGene
+dm2 D. melanogaster dm2 /opt/galaxy/tool-data/ceas_tables/dm2.refGene
+dm3 D. melanogaster dm3 /opt/galaxy/tool-data/ceas_tables/dm3.refGene
+mm8 M. musculus mm8 /opt/galaxy/tool-data/ceas_tables/mm8.refGene
+mm9 M. musculus mm9 /opt/galaxy/tool-data/ceas_tables/mm9.refGene
+hg18 H. sapiens hg18 /opt/galaxy/tool-data/ceas_tables/hg18.refGene
+hg19 H. sapiens hg19 /opt/galaxy/tool-data/ceas_tables/hg19.refGene
diff -r d59bf233d184 -r 012afa77c724 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Dec 09 06:54:34 2014 -0500
@@ -0,0 +1,7 @@
+
+