<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>