# HG changeset patch
# User nikhil-joshi
# Date 1418125843 18000
# Node ID a5b3f7cf458e23d637c862339d4e843372551292

Uploaded

diff -r 000000000000 -r a5b3f7cf458e ceas/README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas/README	Tue Dec 09 06:50:43 2014 -0500
@@ -0,0 +1,2 @@
+You can find the CEAS databases here:
+http://liulab.dfci.harvard.edu/CEAS/download.html
diff -r 000000000000 -r a5b3f7cf458e ceas/ceas.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas/ceas.xml	Tue Dec 09 06:50:43 2014 -0500
@@ -0,0 +1,156 @@
+<tool id="ceas" name="CEAS" version="1.0.2">
+	<description>Get stats on ChIP enrichment and infer genes regulated by binding factors</description>
+
+	<command>
+	mkdir -p "$pdf_out.files_path" &amp;&amp;
+	cd "$pdf_out.files_path" &amp;&amp;
+
+	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&gt; /dev/null
+
+	&amp;&amp;
+
+	#if $analysis_files.wig_or_bed != "wig":
+	mv $pdf_out.files_path/ceas_out.xls $annot_out &amp;&amp;
+	#end if
+	mv $pdf_out.files_path/ceas_out.R $r_out &amp;&amp;
+	mv $pdf_out.files_path/ceas_out.pdf $pdf_out &amp;&amp;
+
+	rm -r "$pdf_out.files_path"
+	</command>
+
+	<inputs>
+	<conditional name="analysis_files">
+		<param name="wig_or_bed" type="select" optional="false" label="Select the type of analysis">
+			<option value="bed" selected="true">Run only ChIP region and gene-centered annotation</option>
+			<option value="wig">Run only average signal profiling</option>
+			<option value="both1">Run both annotation and profiling</option>
+			<option value="both2">Run genome background annotation</option>
+		</param>
+
+		<when value="bed">
+			<param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
+		</when>
+
+		<when value="wig">
+                        <param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
+                </when>
+
+		<when value="both1">
+			<param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
+			<param format="wig" name="chip_wig" type="data" label="WIG file with ChiP enrichment signal"/>
+		</when>
+
+		<when value="both2">
+			<param format="bed" name="chip_bed" type="data" label="BED file of ChIP regions"/>
+			<param format="wig" name="chip_wig" type="data" label="WIG file for genome background annotation"/>
+		</when>
+	</conditional>
+
+        <param name="refgene_table" label="Gene annotation table" type="select">
+            <options from_data_table="ceas_refgene_tables">
+                <filter type="sort_by" column="1"/>
+                <validator type="no_options" message="No indexes are available for the selected dataset"/>
+            </options>
+        </param>
+
+	<param format="bed" name="extra_bed" type="data" optional="true" label="BED file of extra regions of interest (e.g. non-coding regions)"/>
+
+	<param name="sizes" type="integer" optional="true" label="Promoter (also downstream) sizes for ChIP region annotation" help="Three comma-separated integers or a single integer. Leave blank for default."/>
+
+	<param name="bisizes" type="integer" optional="true" label="Bidirectional promoter sizes for ChIP region annotation" help="Two comma-separated integers or a single integer. Leave blank for default."/>
+
+	<param name="span" type="integer" optional="true" label="Span from TSS and TTS in the gene-centered annotation" help="Leave blank for default."/>
+	<param name="pfres" type="integer" optional="true" label="WIG profiling resolution" help="Leave blank for default."/>
+	<param name="reldist" type="integer" optional="true" label="Relative distance to TSS/TTS in wig profiling" help="Leave blank for default."/>
+
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="annot_out" label="Gene-centered annotation from ${tool.name} on ${on_string} (XLS)">
+		<filter>(analysis_files['wig_or_bed'] != 'wig')</filter>
+		</data>
+		<data format="txt" name="r_out" label="R script for graph results from ${tool.name} on ${on_string}" />
+		<data format="pdf" name="pdf_out" label="Graph results from ${tool.name} on ${on_string} (PDF)" />
+	</outputs>
+
+	<help>
+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
+	</help>
+
+</tool>
diff -r 000000000000 -r a5b3f7cf458e ceas/ceas_tables.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas/ceas_tables.loc.sample	Tue Dec 09 06:50:43 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