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<tool id="circosJunctions" name="Integrative Plot" version="1.56">
	<description> Create a Circos plot with Complete Genomics and/or SNParray data </description>


	<requirements>
		<requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
		<requirement type="package" version="0.64">circos</requirement>	    
	</requirements>
	

	<command interpreter="bash">
	galaxy_runCircos.sh 
		$junctions 
		$probes 
		$snps 
		$variants 
		#if $imageformat == "png"
			$wg_out 
			$montage_out 			
		#else
			$wg_out2 
			$montage_out2			
		#end if
		$chromosomes_out 
		$reference
		$custom_out
		"$custom.region"		
		$genetrack
		$imageformat
		\$CIRCOS_SCRIPT_PATH/scripts
		\$CIRCOS_SCRIPT_PATH/config
	</command>
	
	<inputs>

		<param name="reference" type="select" label="Reference">
				<option value="hg18" selected="true"> HG18 (build 36) </option>
				<option value="hg19"> HG19 (build 37) </option>		
		</param>
		<param name="junctions" type="data" 	optional="true" 	format="tabular" label="CG Junctions file"/>
		<param name="variants"  type="data" 	optional="true" 	format="tabular" label="Variants list (e.g. output from CG listvariants)"/>	
		
		<param name="snps" 		type="data" 	optional="true" 	format="tabular" label="Illumina (Nexus) snps.txt file"/>	
		<param name="probes"  	type="data" 	optional="true" 	format="tabular" label="Illumina (Nexus) probes.txt file"/>	
				
		<param name="wg"  		type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="true" 	label="Generate Whole-Genome plot?"/>
		<param name="chrplots" 	type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="false" label="Also generate per-chromosome plots?"/>
		<param name="montage"  	type="boolean" 	truevalue="Y" 	falsevalue="N" 	checked="false" label="Also generate montage of per-chromosome plots?"/>
		<param name="genetrack" type="boolean" 	truevalue="yes" falsevalue="no" checked="false" label="Add ImpactedGenes track (only for the per-chromosome or custom plots)" help="Shows which genes are impacted by the SV events (junctions)"/>
	
		<conditional name="custom">
   			<param name="plot" type="select" label="Create a plot of a custom region?">
				<option value="N" selected="true"> No </option>
				<option value="Y"> Yes </option>		
			</param>			      			
   			<when value="N">
      			<param name="region" type="hidden" value="None" />
   			</when>
   			<when value="Y">
     			<param name="region" type="text" value="None" label="Region" help="For example: 'chr5;chr6;chrX' or 'chr12:12345-34567' or 'chr5:0-100,200-333;chrX:34567-78347'">
				<sanitizer sanitize="False"/>
				</param>
   			</when>
		</conditional>		
		
		<param name="imageformat" type="select" label="Image Format">
				<option value="png" selected="true"> PNG </option>
				<option value="svg"> SVG </option>		
		</param>
		
		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
		
	</inputs>

  <outputs>
   	<data format="png" name="wg_out" 		label="Whole genome plot on ${on_string}">					<filter> imageformat == "png" </filter> <filter> wg </filter> </data>	
    <data format="png" name="montage_out" 	label="Chromosomes_montage on ${on_string}">				<filter> imageformat == "png" </filter> <filter> montage </filter> </data>
	<data format="png" name="custom_out"   	label="Plot of region ${custom.region} on ${on_string} "> 	<filter> imageformat == "png" </filter> <filter> custom['plot'] == "Y" </filter> </data>	
	
	<data format="svg" name="wg_out2" 		label="Whole genome plot on ${on_string}">					<filter> imageformat == "svg" </filter>	<filter> wg </filter> </data>	
    <data format="svg" name="montage_out2" 	label="Chromosomes_montage on ${on_string}">				<filter> imageformat == "svg" </filter> <filter> montage </filter> </data>
	<data format="svg" name="custom_out2"  	label="Plot of region ${custom.region} on ${on_string} "> 	<filter> imageformat == "svg" </filter>	<filter> custom['plot'] == "Y" </filter> </data>
	
	
	<data format="gzip" name="chromosomes_out" label="Chromosome plots on ${on_string}"> <filter> chrplots </filter> </data>
  </outputs>

	<help> 


	</help>

</tool>