<tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.6">
	<description> Filter SVs based on presence in VN set </description>
	
	<requirements>		
		<requirement type="package" version="1.7">cgatools</requirement>
	</requirements>
	
	<command interpreter="bash">
	JunctionDiff-vs-background.sh 
		--variants $variants 
		--reference ${reference.fields.reference_crr_cgatools} 
		#if $virtnorm.VNset == "diversity"
			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list} 
		#else
			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list_1000G} 
		#end if
		--cgatools_binary cgatools
		--outputfile_filtered $output_filtered 
		--scoreThresholdA $scoreThresholdA 
		--scoreThresholdB $scoreThresholdB 
		--distance $distance 
		--minlength $minlength					
	</command>
	
	<inputs>
		<!--select build-->
		<param name="reference" type="select" label="Select Build">
			<options from_data_table="virtual_normal_correction" />
			<filter type="data_meta" ref="variants" key="dbkey" column="0" />
		</param>
		<conditional name="virtnorm" >
		<param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples">
			<option value="diversity" selected="true"> CG Diversity Panel and trios (54 Genomes) (hg18/hg19) </option>
			<option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
		</param>
		</conditional>
		<param name="variants" type="data" format="tabular" label="CG Junctions file"/>
		<param name="scoreThresholdA" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from input genome"/>
		<param name="scoreThresholdB" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from background genomes"/>
		<param name="distance" type="text" value="200" label="Maximum distance between coordinates of potentially compatible junctions."/>		
		<param name="minlength" type="text" value="500" label="Minimum deletion junctions length to be included into the difference file."/>
		<param name="report" type="select"  label="Generate report file?">
			<option value="N" selected="true"> No </option>
			<option value="Y"> Yes </option>
		</param>
		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>		
	</inputs>

  <outputs>
       <data format="tabular" name="output_filtered" label="${fname} Filtered junctions for ${tool.name} on  ${on_string}"/>		
       <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on  ${on_string}">
       	<filter> report == "Y" </filter>
       </data>			  
  </outputs>

	<help> 
**What it does**



**Input Files**
Complete Genomics Junctions file

**Output Files**
Junctions remaining after filtering


	</help>

</tool>