<tool id="cg_junctiondiff" name="JunctionDiff" version="1.7.1">

	<description>Reports difference between junction calls</description> <!--adds description in toolbar-->

	<requirements>		
		<requirement type="package" version="1">cgatools17</requirement>
	</requirements>

	<command > <!--run executable-->
		cgatools | head -1;
		cgatools junctiondiff --beta 
		--reference ${crr.fields.crr_path} 
		--junctionsA $inputA 
		--junctionsB $inputB 
		--scoreThresholdA $scoreA
		--scoreThresholdB $scoreB
		--distance $distance
		--minlength $minlength
		$stat  
		--output-prefix cg_ 
		;
		mv cg_diff-* cg_diff.tsv
	</command>

	<inputs>		
		<!-- reference -->
		<param name="crr" type="select" label="Reference Build">
			<options from_data_table="cg_anno_files" />
		</param>				

		<!--input files-->
		<param name="inputA" type="data" format="tabluar" label="Junction file A"/>			
		<param name="inputB" type="data" format="tabluar" label="Junction file B"/>		
		
		<!--parameters-->
		<param name="stat" type="select" label="Print input file stats">
			<option value="">no</option>
			<option value="--statout">yes</option>
		</param>

		<param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/>
		<param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/>
		<param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/>
		<param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500"/>
	
		<!-- 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="corrected_junctions" from_work_dir="cg_diff.tsv" label="$fname ${tool.name} on ${on_string}: diff"/>
		<data format="tabular" name="report" from_work_dir="cg_report.tsv" label="$fname ${tool.name} on ${on_string}: report">
			<filter>(stat == '--statout')</filter>
		</data>
	</outputs>
  

	<help>
**What it does**

This tool reports difference between junction calls of Complete Genomics junctions files

**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
		  junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
		
		DESCRIPTION
		  junctiondiff takes two junction files A and B as input and produces the 
		  following output:
		    - "diff-inputFileName" - the junctions from an input file A that are not 
		      present in input file B.
		    - "report.txt" - a brief summary report (if --statout is used)
				
		  Two junctions are considered equivalent if:
		    - they come from different files
		    - left and right positions of one junction are not more than "--distance"
		      bases apart from the corresponding positions of another junction
		    - the junction scores are equal or above the scoreThreshold
		    - they are on the same strands
		
		OPTIONS
		  -h [ --help ] 
		      Print this help message.
		
		  --beta 
		      This is a beta command. To run this command, you must pass the --beta 
		      flag.
		
		  -s [ --reference ] arg
		      Reference file.
		
		  -a [ --junctionsA ] arg
		      input junction file A.
		
		  -b [ --junctionsB ] arg
		      input junction file B.
		
		  -A [ --scoreThresholdA ] arg (=10)
		      score threshold value for the input file A.
		
		  -B [ --scoreThresholdB ] arg (=0)
		      score threshold value for the input file B.
		
		  -d [ --distance ] arg (=200)
		      Max distance between coordinates of potentially compatible junctions.
		
		  -l [ --minlength ] arg (=500)
		      Minimum deletion junction length to be included into the difference 
		      file.
		
		  -o [ --output-prefix ] arg
		      The path prefix for all the output reports.
		
		  -S [ --statout ] 
		      (Debug) Report various input file statistics. Experimental feature.
		
		SUPPORTED FORMAT_VERSION
		  1.5 or later
	</help>
</tool>