comparison CG_cgatools/tools/cgatools/junctiondiff.xml @ 0:ffb2b0244ab2 draft

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<tool id="cga_junctiondiff" name="junctiondiff(beta)" version="0.0.1">

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

  <requirements>
  	<requirement type="binary">cgatools</requirement>
  </requirements>

  <command> <!--run executable-->
  	cgatools junctiondiff --beta -h
  </command>

  <outputs>
  	<data format="tabular" name="output" />
  </outputs>
  
  <inputs>
  </inputs>

  <help>
  
**What it does**

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

cgatools: http://sourceforge.net/projects/cgatools/files/

-----

**cgatools Manual**::

		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>