diff cgatools_suite/tools/cgatools/junctiondiff.xml @ 7:96829b1b73ea draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools_suite/tools/cgatools/junctiondiff.xml	Wed Jun 06 16:58:26 2012 -0400
@@ -0,0 +1,88 @@
+<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>