<tool id="junctions2events" name="Junctions2Events" version="1.7.1">
	<description> Groups related junctions and annotates each group with information about the structural rearrangement (event) that these junctions represent </description>
	  
	<requirements>		
		<requirement type="package" version="1">cgatools17</requirement>
	</requirements>
  	
	<command>
		cgatools | head -1;
		cgatools junctions2events --beta 
		--reference ${refs.fields.crr_path} 
		--junctions $junctions 
		#if $alljunctions
			--all-junctions $alljunctions
		#end if
		--repmask-data ${refs.fields.repmask_path}
		--gene-data ${refs.fields.genedata_path}
		#if $more_options.options_type_selector == "more"
			--regulatory-region-length $regreglen
			--contained-genes-max-range $contgenmax
			--max-related-junction-distance $maxreljdist
			--max-pairing-distance $maxpairdist
			--max-copy-target-length $maxcopylen
			--max-simple-event-distance $maxsed
			#if $more_options.mobelname
				--mobile-element-names $mobelname
			#end if
			--max-distance-to-m-e $maxdisttome
		#end if
	</command>
	
	<inputs>
		<!-- select reference  -->
		<param name="refs" type="select" label="Reference Build">
			<options from_data_table="cg_anno_files" />
		</param>

		<!-- select junction files  -->
		<param name="junctions" type="data" format="tabular" label="Junctions file (allJunctions of highConfidenceJunction)"/>		
		<param name="alljunctions" type="data" format="tabular" optional="true" label="Optional: allJunctions file"/>

		<!-- advanced settings  -->
		<conditional name="more_options">
   			<param name="options_type_selector" type="select" label="Advanced Options">
      			<option value="hide" selected="True">Less options</option>
      			<option value="show">More options</option>
   			</param>
   			<when value="less">
      			<!-- no options -->
   			</when>
   			<when value="show">
     			<param name="regreglen"  	type="integer" value="7500" min="0" label="regulatory region length" help="Length of the region upstream of the gene that may contain regulatory sequence for the gene" />
				<param name="contgenmax" 	type="integer" value="-1" min="0" label="contained genes max range" help="Maximum length of a copy or deletion event to annotate with all genes that overlap the copied or deleted segment. (Negative value causes all events to be annotated regardless of the length)" />
		 		<param name="maxreljdist"  	type="integer" value="700" min="0" label="max related junctions distance" help="Junctions occurring within this distance are presumed to be related" />
		 		<param name="maxpairdist" 	type="integer" value="10000000" min="0" label="max pairing distance" help="Maximum allowed distance between junction sides wshen searching for paired junctions caused by the same event." />
				<param name="maxcopylen" 	type="integer" value="1000" min="0" label="max copy target length" help="Pairs of junctions will be classified as a copy event only if the length of the implied copy target region is below this threshold." />
				<param name="maxsed" 		type="integer" value="10000000" min="0" label="max simple event distance" help="When given a choice of identifying an event as a mobile element copy or as a simple deletion/duplication, prefer the latter explanation if the length of the affected sequence is below this threshold" />
				<param name="mobelname" 	type="select" multiple="true" display="checkboxes" label="mobile element names" help="Names of mobile elements that are known to be active and sometimes copy flanking 3' sequence" >
					<option value="L1HS"> L1HS </option>
					<option value="AluY"> AluY </option>
					<option value="SVA">  SVA </option>
				</param>
				<param name="maxdisttome" 	type="integer" value="2000" min="0" label="max distance to ME" help="Maximum allowed distance from the junction side to the element when searching for a mobile element related to a junction" />
	   		</when>
		</conditional>

		<!-- prefix for output file so you dont have to manually rename history items -->
   		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
	</inputs>

	<outputs>
		<data format="tabular" name="annotatedjunctions" from_work_dir="AnnotatedJunctions.tsv" label="$fname AnnotatedJunctions file of ${tool.name} on ${on_string}"/>
		<data format="tabular" name="events" from_work_dir="Events.tsv" label="$fname Events file of ${tool.name} on ${on_string}"/>
	</outputs>

	<help>
	
**What it does**  

This tool searches for groups of related junctions and for every group 
attempts to determine the event that caused the junctions.

**cgatools 1.7.1 Documentation**

Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf

Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf

**Command line reference**::

	COMMAND NAME
		junctions2events - Groups and annotates junction calls by event type.


	OPTIONS
	  -h [ --help ] 
			Print this help message.

	  --beta 
			This is a beta command. To run this command, you must pass the --beta 
			flag.

	  --reference arg
			Reference file.

	  --output-prefix arg
			The path prefix for all output reports.

	  --junctions arg
			Primary input junction file.

	  --all-junctions arg
			Superset of the input junction file to use when searching for the 
			related junctions. The default is to use only the junctions in the 
			primary junction file.

	  --repmask-data arg
			The file that contains repeat masker data.

	  --gene-data arg
			The file that contains gene location data.

	  --regulatory-region-length arg (=7500)
			Length of the region upstream of the gene that may contain regulatory 
			sequence for the gene. Junctions that connect this region to another 
			gene will be annotated as a special kind of gene fusion.

	  --contained-genes-max-range arg (=-1)
			Maximum length of a copy or deletion event to annotate with all genes 
			that overlap the copied or deleted segment. Negative value causes all 
			events to be annotated regardless of the length.

	  --max-related-junction-distance arg (=700)
			Junctions occurring within this distance are presumed to be related.

	  --max-pairing-distance arg (=10000000)
			When searching for paired junctions caused by the same event, maximum 
			allowed distance between junction sides.

	  --max-copy-target-length arg (=1000)
			Pairs of junctions will be classified as a copy event only if the 
			length of the implied copy target region is below this threshold.

	  --max-simple-event-distance arg (=10000000)
			When given a choice of explaining an event as a mobile element copy or 
			as a simple deletion/duplication, prefer the latter explanation if the 
			length of the affected sequence if below this threshold.

	  --mobile-element-names arg (=L1HS,SVA)
			Comma-separated list of the names of the mobile elements that are known
			to be active and sometimes copy flanking 3' sequence.

	  --max-distance-to-m-e arg (=2000)
			When searching for a mobile element related to a junction, maximum 
			allowed distance from the junction side to the element.

	  --max-related-junction-output arg (=100)
			Maximum number of related junctions included into annotation field


	SUPPORTED FORMAT_VERSION
		1.5 or later

	</help>
</tool>