# HG changeset patch
# User nikhil-joshi
# Date 1418125984 18000
# Node ID d59bf233d184ff390f596ab24beafaa4e02170e3
# Parent  a5b3f7cf458e23d637c862339d4e843372551292
Deleted selected files

diff -r a5b3f7cf458e -r d59bf233d184 ceas/README
--- a/ceas/README	Tue Dec 09 06:50:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-You can find the CEAS databases here:
-http://liulab.dfci.harvard.edu/CEAS/download.html
diff -r a5b3f7cf458e -r d59bf233d184 ceas/ceas.xml
--- a/ceas/ceas.xml	Tue Dec 09 06:50:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-<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 a5b3f7cf458e -r d59bf233d184 ceas/ceas_tables.loc.sample
--- a/ceas/ceas_tables.loc.sample	Tue Dec 09 06:50:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-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